X-RAY DIFFRACTION Experimental Data & Validation


Lost? View more X-Ray Crystallographic info.

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 9
Temperature 298.0
Details 100 mM Tris-HCl pH 9.0, 4 mM DTT, 1.5% saturated MgSO4, 16% ethylene glycol, 20% mPEG2K, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 123.37 α = 90
b = 123.37 β = 90
c = 35.4 γ = 120
Symmetry
Space Group P 61

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 90
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE MAR scanner 345 mm plate -- 1999-07-15
Diffraction Radiation
Monochromator Protocol
MIRRORS POLAR 0.000 SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL9-1 0.78 SSRL BL9-1

Data Collection

Overall
Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot
0.92 30 95.9 -- 0.053 -- 2.84 213629 204938 5.0 5.0 26.5
High Resolution Shell
Resolution (High) Resolution (Low) Percent Possible (All) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All)
0.9194 0.95 88.6 0.42 -- -- -- --

Refinement

Statistics
Structure Solution Method Refinement High Resolution Refinement Low Resolution Cut-off Sigma (I) Cut-off Sigma (F) Number of Reflections (All) Number of Reflections (Observed) Number of Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work R-Free R-Free Selection Details
MOLECULAR REPLACEMENT 0.9194 24.511 -- 1.34 204931 204917 10253 95.92 -- 0.1255 0.1248 0.139 --
High Resolution Shell
Refinement method Shell Resolution (High) Shell Resolution (Low) # of Reflections (Observed) # of Reflections (R-Free) # of Reflections (R-Work) R-Factor (R-Work) R-Factor (R-Free) R-Factor (R-Free Error) Percent Reflections (Observed)
X Ray Diffraction 0.9194 0.9298 -- 288 5717 0.2196 0.2396 -- 84.0
X Ray Diffraction 0.9298 0.9408 -- 315 6078 0.1972 0.2195 -- 91.0
X Ray Diffraction 0.9408 0.9523 -- 313 6184 0.178 0.1881 -- 92.0
X Ray Diffraction 0.9523 0.9643 -- 337 6337 0.1714 0.1783 -- 94.0
X Ray Diffraction 0.9643 0.977 -- 321 6341 0.161 0.1774 -- 94.0
X Ray Diffraction 0.977 0.9904 -- 342 6415 0.1554 0.1653 -- 96.0
X Ray Diffraction 0.9904 1.0045 -- 319 6459 0.1474 0.1573 -- 95.0
X Ray Diffraction 1.0045 1.0195 -- 333 6473 0.1358 0.1494 -- 96.0
X Ray Diffraction 1.0195 1.0355 -- 331 6517 0.1255 0.1498 -- 96.0
X Ray Diffraction 1.0355 1.0524 -- 333 6537 0.1184 0.1293 -- 97.0
X Ray Diffraction 1.0524 1.0706 -- 372 6456 0.1113 0.1345 -- 96.0
X Ray Diffraction 1.0706 1.09 -- 347 6473 0.104 0.1219 -- 97.0
X Ray Diffraction 1.09 1.111 -- 349 6539 0.1033 0.1095 -- 96.0
X Ray Diffraction 1.111 1.1337 -- 362 6480 0.0981 0.1141 -- 97.0
X Ray Diffraction 1.1337 1.1583 -- 334 6497 0.0946 0.1148 -- 96.0
X Ray Diffraction 1.1583 1.1853 -- 372 6459 0.0974 0.1107 -- 96.0
X Ray Diffraction 1.1853 1.2149 -- 359 6470 0.1 0.1188 -- 96.0
X Ray Diffraction 1.2149 1.2478 -- 318 6447 0.0976 0.1071 -- 95.0
X Ray Diffraction 1.2478 1.2845 -- 329 6451 0.1 0.1151 -- 95.0
X Ray Diffraction 1.2845 1.3259 -- 327 6434 0.0999 0.114 -- 95.0
X Ray Diffraction 1.3259 1.3733 -- 333 6606 0.1 0.1186 -- 98.0
X Ray Diffraction 1.3733 1.4283 -- 384 6719 0.1001 0.1159 -- 100.0
X Ray Diffraction 1.4283 1.4933 -- 355 6750 0.0981 0.1213 -- 100.0
X Ray Diffraction 1.4933 1.572 -- 347 6741 0.1013 0.111 -- 100.0
X Ray Diffraction 1.572 1.6705 -- 314 6793 0.1187 0.1478 -- 99.0
X Ray Diffraction 1.6705 1.7994 -- 366 6643 0.1243 0.1352 -- 98.0
X Ray Diffraction 1.7994 1.9805 -- 337 6661 0.122 0.1461 -- 97.0
X Ray Diffraction 1.9805 2.2669 -- 363 6592 0.1211 0.1329 -- 97.0
X Ray Diffraction 2.2669 2.8553 -- 388 6778 0.1275 0.1436 -- 99.0
X Ray Diffraction 2.8553 24.5198 -- 365 6617 0.1551 0.1599 -- 94.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 17.0195
Anisotropic B[1][1] 0.0
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.0
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.0
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.008
f_chiral_restr 0.08
f_dihedral_angle_d 12.775
f_angle_d 1.311
f_bond_d 0.017
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2267
Nucleic Acid Atoms 0
Heterogen Atoms 27
Solvent Atoms 427

Software

Computing
Computing Package Purpose
HKL Data Collection
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
EPMR Structure Solution
PHENIX (phenix.refine: 1.8.1_1168) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
phenix refinement
EPMR version: 2.1 molecular replacement
SCALEPACK data reduction