Granulocyte-macrophage colony stimulating factor
Summary of this structure solution:
This is an MIR dataset with 4800 reflections to 3.5 A, 4 derivatives, and 254 amino acids. The data is courtesy of Kay Diederichs. The derivatives are not that good and the overall figure of merit of the structure is only 0.54 to 3.5 A. Using all the data and including anomalous differences, SOLVE took 18 minutes to solve this MIR problem on a DEC Alpha 500 MHz workstation. Solve only used 3 of the 4 derivatives in phasing.
Solve.setup file listing basic information about the crystals:
cell 47.6 59.1 126.7 90 90 90 symfile p212121.sym resolution 20 3.5Input script file used to run SOLVE on Granulocyte-macrophage colony stimulating factor
#!/bin/csh # # set CCP4 and SOLVETMPDIR variables: # setenv CCP4_OPEN UNKNOWN setenv SOLVETMPDIR /var/tmp setenv SYMOP /usr/local/lib/solve/symop.lib setenv SYMINFO /usr/local/lib/solve/syminfo.lib # solve <<EOD > solve.log ! solve.com for gmf 7-25-97 ! include known h.a. sites for comparison and fft map as well logfile mir.logfile ! write out most information to this file. @solve.setup title gm native + 4 derivatives ! readformatted premerged checksolve comparisonfile gm_offset.fft rawnativefile gmnat.fmt derivative 1 inano noanorefine label deriv 1 gm18 pcmbs rawderivfile gm18.fmt ATOMNAME Hg nsolsite_deriv 2 XYZ 0.4069387 0.5974227 0.1901610 XYZ 0.4322624 0.5161777 0.2020042 derivative 2 inano noanorefine label deriv 2 gmPt(EtNH2)2Cl2 derivative #40 rawderivfile gm40.fmt ATOMNAME Pt nsolsite_deriv 6 derivative 3 inano noanorefine label mersalyl acid # 52 rawderivfile gm52.fmt ATOMNAME Hg nsolsite_deriv 2 XYZ 0.9070011 0.4427668 0.1972121 XYZ 0.4240658 0.6003970 0.1951167 derivative 4 inano noanorefine label HgI2 #57 rawderivfile gm57.fmt ATOMNAME Hg nsolsite_deriv 3 XYZ 0.9747854 0.4725027 0.2089491 XYZ 0.3438405 0.6067868 0.1840420 acceptance 0.35 ! accept new sites with ~50% of height of avg scale_native scale_mir analyze_mir SOLVE EODSummary information from the "solve.prt" output file produced after completion of the automated structure determination
Selenium atom occupancy, coordinates, and thermal factors, andCross-validation fouriers calculated with all heavy atoms inall derivs except the site being evaluated and any sites equivalent to it.
(Peak height is height of peak at this position/rms of map)
Site x y z occ B -- PEAK HEIGHT --
Deriv 1:
1 0.404 0.600 0.192 0.130 60.000 14.80
2 0.923 0.440 0.200 0.112 60.000 12.27
Deriv 2:
Deriv 3:
1 0.423 0.600 0.195 0.169 60.000 21.90
2 0.908 0.443 0.197 0.223 60.000 24.02
Deriv 4:
1 0.973 0.481 0.210 0.126 60.000 12.80
2 0.326 0.568 0.188 0.052 16.111 9.09
3 0.357 0.637 0.182 0.040 25.935 3.11
Figure of merit versus resolution
DMIN: TOTAL 11.16 7.54 6.04 5.18 4.61 4.19 3.87 3.61 N: 4801 297 418 525 589 663 713 778 818 MEAN FIG MERIT: 0.54 0.70 0.76 0.73 0.64 0.52 0.48 0.42 0.34List of sites analyzed for compatibility with difference Patterson
(Height is 1000 x height of peak in Patterson/rms of map. Predicted height is expected height based on occupancy of sites)
Derivative 1:
PEAK X Y Z OPTIMIZED
RELATIVE OCCUPANCY
1 0.406 0.597 0.191 47.139
2 0.927 0.438 0.198 40.744
Evaluation of this test soln with 2 sites after optimizing
occupancy of each site
Cross-vectors for sites 1 and 1 (excluding origin; 1000 = 1 sigma):
# U V W HEIGHT PRED HEIGHT SYMM#
1 -0.312 -1.194 0.500 4539.24 4444.25 2
2 -0.812 0.500 0.118 2537.75 4444.25 2
3 0.500 -0.694 -0.382 4848.71 4444.25 2
Cross-vectors for sites 2 and 1 (excluding origin; 1000 = 1 sigma):
# U V W HEIGHT PRED HEIGHT SYMM#
1 0.521 -0.160 0.007 4568.46 1920.64 1
2 -0.833 -1.035 0.507 4088.19 1920.64 1
3 -1.333 0.340 0.111 3195.59 1920.64 1
4 1.021 -0.535 -0.389 2322.98 1920.64 1
Cross-vectors for sites 2 and 2 (excluding origin; 1000 = 1 sigma):
# U V W HEIGHT PRED HEIGHT SYMM#
1 -1.354 -0.875 0.500 1348.34 3320.13 2
2 0.500 -0.375 -0.396 3381.48 3320.13 2
Total of 1 of 11 patterson peaks used more than once.
Overall quality of this Patterson soln = 5946.31
Overall quality of the fit to patterson = 1.38812
Avg normalized peak height = 1792.88
(... etc for derivatives 2,3,4). .
Summary of scoring for this solution:
Summary of scoring for this solution: -- over many solutions-- -- this solution -- Pattersons: 1.87 0.500 3.82 3.89 Cross-validation Fourier: 6.63 3.49 36.3 8.51 NatFourier CCx100: 12.4 5.31 32.8 3.83 Mean figure of meritx100: 0.000E+00 7.53 53.5 7.11 Correction for Z-scores: -3.92 Overall Z-score value: 19.4Tail end of the solve.status file:
*************************************************************************** SOLVE STATUS 07-oct-00 10:18:51 DATASET TITLE: gm native + 4 derivatives TIME ELAPSED: 18 MIN --------------------------------------------------------------------------- CURRENT STEP:SOLVE MAIN PROGRAM STATUS: DONE --------------------------------------------------------------------------- --------------------------------------------------------------------------- ---TOP SOLUTION FOUND BY SOLVE (<m> = 0.54; score = 19.43) --- Deriv X Y Z OCCUP B HEIGHT/SIGMA 1 0.404 0.600 0.192 0.130 60.0 14.8 1 0.923 0.440 0.200 0.112 60.0 12.3 3 0.423 0.600 0.195 0.169 60.0 21.9 3 0.908 0.443 0.197 0.223 60.0 24.0 4 0.973 0.481 0.210 0.126 60.0 12.8 4 0.326 0.568 0.188 0.052 16.1 9.1 4 0.357 0.637 0.182 0.040 25.9 3.1 TIME REQUIRED TO OBTAIN THIS SOLUTION: 16 MIN --------------------------------------------------------------------------- CURRENT RESOLUTION: 3.5 A. FINAL RESOLUTION: 3.5 A.