[Protein-crystallography] For Help

czl at agri.mbox.media.kyoto-u.ac.jp czl at agri.mbox.media.kyoto-u.ac.jp
Mon Jun 26 04:02:57 EST 2006


Dear all:
  I am beginner working on a structure of polysaccharide hydrolase with a MW of 96 KDa belonging to Orthorhombic (Unit cell a=97, b=120, and c=207). Two MAD datasets  were collected. The resolution limit of the datasets were 2.6 and 2.8 A respectively. But the density maps calculated with Solve were both very bad. The followings are the part of the solve log files. 

For Dataset I
Data were colleted at 2 wavelenghth.

Space group name from file name is: p212121   
 Rescaling standard dataset to put it on approximate absolute scale.  NRES = 800;  <F**2> expected =   392000.
 ;  <F**2> observed in lowest resolution shell =   1818.30225
   ... Scale factor =   215.585724
 
  ** Completeness of Fbar data at each wavelength: ** 

 Completeness of dataset  1  ( F >   2. * sigma)
 set 1 with 25 se atoms, lambda 1  
 Reflections observed:
                    Possible  Found     % complete
 shell     dmin
    1     5.200      9705      9681      99.8
    2     3.900     13033     12989      99.7
    3     3.640      5111      5085      99.5
    4     3.445      4946      4904      99.2
    5     3.250      6171      6087      98.6
    6     3.120      5015      4906      97.8
    7     2.990      5885      5764      97.9
    8     2.860      6997      6751      96.5
    9     2.730      8388      7855      93.6
   10     2.600     10159      9236      90.9
 total              75410     73258      97.1

 Completeness of dataset  at lambda 2  ( F >   2. * sigma)
 
lambda 2

Reflections observed:
                    Possible  Found     % complete
 shell     dmin
    1     5.200      9705      9563      98.5
    2     3.900     13033     12901      99.0
    3     3.640      5111      5051      98.8
    4     3.445      4946      4872      98.5
    5     3.250      6171      6048      98.0
    6     3.120      5015      4860      96.9
    7     2.990      5885      5679      96.5
    8     2.860      6997      6681      95.5
    9     2.730      8388      7746      92.3
   10     2.600     10159      8752      86.2
 total              75410     72153      95.7

** R-factors for F-bar data dispersive  differences **


 Dispersive differences lambda  2 - lambda  1 (Delta f-prime =   4.5 )


 Differences by shell:

  shell   dmin    nobs      Fbar      R     scale    SIGNAL  NOISE   S/N

    1     5.200  9509     477.163     0.039   1.000  23.33   4.59   5.08
    2     3.900 12839     547.445     0.028   1.000  18.00   5.68   3.17
    3     3.640  5018     481.398     0.028   1.000  15.79   6.37   2.48
    4     3.445  4840     446.935     0.029   1.000  14.46   7.06   2.05
    5     3.250  5999     389.674     0.031   1.000  13.10   7.86   1.67
    6     3.120  4817     335.666     0.036   1.000  12.03   8.96   1.34
    7     2.990  5625     300.516     0.039   1.000  10.79   9.70   1.11
    8     2.860  6574     269.729     0.042   1.000   8.98  11.08   0.81
    9     2.730  7520     233.048     0.049   1.000   6.12  12.76   0.48
   10     2.600  8422     217.885     0.051   1.000   0.00  14.01   0.00

 Total:         71163     381.526     0.035   1.000  14.42   9.21   2.01

 Recommended resolution cut-off =    2.60

 Anomalous differences lambda  1 (f" =   4.80000019)

 Differences by shell:

  shell   dmin    nobs      Fbar      R     scale    SIGNAL  NOISE   S/N
    1     5.200  7955     478.585     0.064   1.000  37.20   7.25   5.13
    2     3.900 11422     550.020     0.044   1.000  28.75   9.24   3.11
    3     3.640  4535     482.168     0.045   1.000  24.60  10.33   2.38
    4     3.445  4389     448.911     0.047   1.000  23.25  11.23   2.07
    5     3.250  5438     389.837     0.049   1.000  20.37  12.28   1.66
    6     3.120  4358     338.431     0.054   1.000  17.97  13.88   1.29
    7     2.990  5120     302.859     0.060   1.000  16.96  14.95   1.13
    8     2.860  5893     272.366     0.064   1.000  14.06  16.73   0.84
    9     2.730  6676     236.003     0.073   1.000   9.43  18.96   0.50
   10     2.600  7624     220.997     0.075   1.000   0.00  20.50   0.00

 Total:         63410     382.547     0.055   1.000  22.63  14.03   1.97

 Recommended resolution cut-off =    2.60

 Anomalous differences lambda  2 (f" =   0.5)

 Differences by shell:

  shell   dmin    nobs      Fbar      R     scale    SIGNAL  NOISE   S/N

    1     5.200  7949     478.634     0.013   1.000   6.50   4.51   1.44
    2     3.900 11418     550.241     0.013   1.000   7.02   5.78   1.22
    3     3.640  4523     483.174     0.016   1.000   7.17   6.56   1.09
    4     3.445  4340     450.320     0.017   1.000   6.93   7.09   0.98
    5     3.250  5371     392.954     0.020   1.000   6.64   7.77   0.85
    6     3.120  4264     341.815     0.024   1.000   5.86   8.75   0.67
    7     2.990  4932     305.013     0.028   1.000   5.11   9.61   0.53
    8     2.860  5628     277.272     0.031   1.000   3.52  10.58   0.33
    9     2.730  6348     240.449     0.039   1.000   1.53  12.06   0.13
   10     2.600  7105     224.534     0.046   1.000   0.00  13.22   0.00

 Total:         61878     387.563     0.021   1.000   5.59   8.86   0.76

 Recommended resolution cut-off =    2.60

           CORRELATION FOR
           WAVELENGTH PAIRS 
 DMIN    1 VS 2

 5.20     0.47
 3.90     0.36
 3.64     0.26
 3.44     0.27
 3.25     0.26
 3.12     0.20
 2.99     0.16
 2.86     0.14
 2.73     0.14
 2.60     0.08

 ALL      0.27
 
Final refined values of fprime and fdoubleprime

 Form factors at lambda =   0.9792
 f-prime =  -8.50
 f"      =  15.22

 Form factors at lambda =   0.9952
 f-prime =  -4.00
 f"      =   1.87
FIGURE OF MERIT <       0.1   0.2   0.3   0.4   0.5   0.6   0.7  0.8   0.9   1.0
 # OF REFLECTIONS      5827  3953  4270  4575  4881  5024  5097  5024  5368 29948

 FIGURE OF MERIT WITH RESOLUTION
 DMIN:           TOTAL    9.06   5.82   4.58   3.90   3.45   3.13   2.88   2.68
 N:               73967   3876   6318   7960   9284  10404  11384  12143  12598
 MEAN FIG MERIT:   0.67   0.85   0.87   0.83   0.79   0.73   0.64   0.54   0.43

For Dataset II

Space group number is:  19
 Space group name from file name is: p212121   
 Rescaling standard dataset to put it on approximate absolute scale.  NRES = 
 800;  <F**2> expected =   392000.
 ;  <F**2> observed in lowest resolution shell =   598.400085
   ... Scale factor =   655.080139

 --------------------------------------------------

  *** Analysis of this scaled MAD data set *** 

  Fbar,sigma,Delano,sigma for  3 wavelengths written to:
 mad_fbar.scl                                                                    

  F+,sigma,F-,sigma for  3 wavelengths written to:
 mad_fpfm.scl                                                                    

  ** Completeness of Fbar data at each wavelength: ** 

 Completeness of dataset  1  ( F >   2. * sigma)
 set 1 with 28 se atoms, lambda 1
                                                
 Reflections observed:

                    Possible  Found     % complete
 shell     dmin

    1     5.600      7770      7692      99.0
    2     4.200     10389     10309      99.2
    3     3.920      4103      4050      98.7
    4     3.710      3937      3880      98.6
    5     3.500      4887      4816      98.5
    6     3.360      3982      3886      97.6
    7     3.220      4710      4545      96.5
    8     3.080      5592      5336      95.4
    9     2.940      6705      6284      93.7
   10     2.800      8099      7353      90.8

 total              60174     58151      96.6


 Completeness of dataset  2  ( F >   2. * sigma)
 set 2
                                                                        Reflections observed:

                    Possible  Found     % complete
 shell     dmin

    1     5.600      7770      7644      98.4
    2     4.200     10389     10234      98.5
    3     3.920      4103      4024      98.1
    4     3.710      3937      3855      97.9
    5     3.500      4887      4780      97.8
    6     3.360      3982      3857      96.9
    7     3.220      4710      4508      95.7
    8     3.080      5592      5278      94.4
    9     2.940      6705      6180      92.2
   10     2.800      8099      7173      88.6

 total              60174     57533      95.6


 Completeness of dataset  3  ( F >   2. * sigma)
 set 3                                                                           
 Reflections observed:

                    Possible  Found     % complete
 shell     dmin

    1     5.600      7770      7597      97.8
    2     4.200     10389     10247      98.6
    3     3.920      4103      4040      98.5
    4     3.710      3937      3870      98.3
    5     3.500      4887      4773      97.7
    6     3.360      3982      3884      97.5
    7     3.220      4710      4518      95.9
    8     3.080      5592      5294      94.7
    9     2.940      6705      6247      93.2
   10     2.800      8099      7321      90.4

 total              60174     57791      96.0

  ** R-factors for F-bar data dispersive  differences **


 Dispersive differences lambda  2 - lambda  1 (Delta f-prime =   1.35000038 )


 Differences by shell:

  shell   dmin    nobs      Fbar      R     scale    SIGNAL  NOISE   S/N

    1     5.600  7585     478.848     0.026   1.000  14.77   4.76   3.10
    2     4.200 10162     555.376     0.025   0.999  16.13   5.75   2.80
    3     3.920  3991     528.172     0.027   1.000  16.47   6.76   2.44
    4     3.710  3820     491.892     0.029   1.000  16.26   7.47   2.18
    5     3.500  4737     465.015     0.030   1.000  15.28   8.15   1.88
    6     3.360  3815     416.568     0.033   1.000  14.44   9.18   1.57
    7     3.220  4432     372.983     0.035   1.000  12.60  10.55   1.19
    8     3.080  5188     331.492     0.038   1.000  10.64  11.86   0.90
    9     2.940  6040     296.977     0.040   1.000   7.33  13.09   0.56
   10     2.800  6973     261.469     0.046   1.000   0.00  14.97   0.00

 Total:         56743     423.745     0.031   1.000  13.22   9.72   1.73

 Recommended resolution cut-off =    2.80

 Dispersive differences lambda  3 - lambda  1 (Delta f-prime =   4.5 )

 Differences by shell:

  shell   dmin    nobs      Fbar      R     scale    SIGNAL  NOISE   S/N

    1     5.600  7528     478.218     0.042   1.000  24.29   5.15   4.72
    2     4.200 10185     554.469     0.029   1.000  18.91   6.24   3.03
    3     3.920  3992     527.166     0.028   1.000  16.93   7.22   2.34
    4     3.710  3833     491.894     0.029   1.000  16.25   7.99   2.03
    5     3.500  4736     464.924     0.030   1.000  15.46   8.57   1.80
    6     3.360  3835     414.412     0.032   1.000  13.41   9.86   1.36
    7     3.220  4440     372.431     0.035   1.000  12.13  10.98   1.11
    8     3.080  5196     331.379     0.040   1.000  10.68  12.41   0.86
    9     2.940  6078     295.903     0.043   1.000   7.71  13.78   0.56
   10     2.800  7042     259.767     0.049   1.000   0.00  15.77   0.00

 Total:         56865     422.607     0.035   1.000  15.50  10.28   1.94

 Recommended resolution cut-off =    2.80

 Dispersive differences lambda  3 - lambda  2 (Delta f-prime =   5.85000038 )

 Differences by shell:

  shell   dmin    nobs      Fbar      R     scale    SIGNAL  NOISE   S/N

    1     5.600  7505     478.758     0.040   1.000  23.28   5.01   4.65
    2     4.200 10127     555.478     0.029   1.000  19.30   6.06   3.19
    3     3.920  3976     526.936     0.028   1.000  17.22   7.19   2.39
    4     3.710  3810     491.762     0.028   1.000  15.44   7.94   1.95
    5     3.500  4707     465.852     0.030   1.000  15.30   8.53   1.79
    6     3.360  3810     415.456     0.032   1.000  13.50   9.92   1.36
    7     3.220  4405     372.816     0.036   1.000  12.61  11.16   1.13
    8     3.080  5141     332.928     0.038   1.000   9.67  12.51   0.77
    9     2.940  6027     297.986     0.043   1.001   8.14  14.00   0.58
   10     2.800  6902     262.461     0.049   1.000   0.00  15.97   0.00

 Total:         56410     424.111     0.035   1.000  15.36  10.33   1.95

 Recommended resolution cut-off =    2.80

 Anomalous differences lambda  1 (f" =   4.80000019)

 Differences by shell:

  shell   dmin    nobs      Fbar      R     scale    SIGNAL  NOISE   S/N

    1     5.600  6279     480.650     0.045   1.000  26.27   6.69   3.93
    2     4.200  9087     559.047     0.033   1.000  21.72   8.32   2.61
    3     3.920  3618     531.744     0.032   1.000  18.90   9.64   1.96
    4     3.710  3477     490.958     0.035   1.000  18.20  10.85   1.68
    5     3.500  4336     467.008     0.036   1.000  16.93  11.65   1.45
    6     3.360  3507     417.485     0.037   1.000  14.71  13.04   1.13
    7     3.220  4042     374.486     0.042   1.000  13.31  14.43   0.92
    8     3.080  4697     336.508     0.046   1.000  11.02  15.85   0.70
    9     2.940  5475     300.508     0.053   1.000   9.54  17.42   0.55
   10     2.800  6223     265.048     0.059   1.000   0.00  19.33   0.00

 Total:         50741     425.828     0.040   1.000  17.11  13.20   1.61

 Recommended resolution cut-off =    2.80

CORRELATION FOR
           WAVELENGTH PAIRS 
 DMIN    1 VS 2   1 VS 3   2 VS 3

 5.60     0.81     0.42     0.46
 4.20     0.68     0.31     0.33
 3.92     0.58     0.28     0.28
 3.71     0.55     0.22     0.25
 3.50     0.53     0.21     0.21
 3.36     0.48     0.23     0.18
 3.22     0.45     0.16     0.12
 3.08     0.41     0.16     0.11
 2.94     0.43     0.16     0.12
 2.80     0.36     0.09     0.09

 ALL      0.53     0.22     0.20

FIGURE OF MERIT <       0.1   0.2   0.3   0.4   0.5   0.6   0.7   0.8   0.9   1.0
 # OF REFLECTIONS     16398 10592  7892  5982  4751  4089  3496  2982  2212   705

 FIGURE OF MERIT WITH RESOLUTION
 DMIN:           TOTAL    9.68   6.25   4.93   4.19   3.71   3.37   3.10   2.89
 N:               59099   3129   5032   6353   7412   8290   9070   9676  10137
 MEAN FIG MERIT:   0.30   0.51   0.45   0.42   0.39   0.34   0.26   0.18   0.13

Sorry for the length of the letter. But I really need your help. I'd like two know if these 2 datasets can be used to solve structure.

Someone told me to transform the .sca file (scalepak) to .mtz file  and use the .mtz to Sovle the phase. Will this work? Does anyone have such experence?

Zhongli Cui
College of Life Sciences
Nanjing Agricultural University
People's Republic of China  







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