X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.5
Temperature 277.0
Details MPD , pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 400.3 α = 90
b = 400.3 β = 90
c = 214.79 γ = 90
Symmetry
Space Group P 41 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
PIXEL DECTRIS PILATUS 6M -- 2011-02-06
Diffraction Radiation
Monochromator Protocol
LN2 cooled fixed-exit Si(111) monochromator SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SLS BEAMLINE X06SA 0.98 SLS X06SA

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
3.74 50 99.7 0.132 -- -- -- 177718 177718 -3.0 -3.0 138.037
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)
3.74 3.97 98.3 0.016 -- 1.87 -- --

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
FOURIER SYNTHESIS 3.742 49.854 -- 1.99 177681 177681 8970 99.71 0.1393 0.1393 0.1368 0.1873 FROM PDB ENTRY 2VQE
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 3.742 3.7845 -- 296 5103 0.2674 0.3159 -- 92.0
X Ray Diffraction 3.7845 3.829 -- 301 5581 0.2414 0.2971 -- 100.0
X Ray Diffraction 3.829 3.8757 -- 330 5533 0.2285 0.2817 -- 100.0
X Ray Diffraction 3.8757 3.9247 -- 307 5582 0.2425 0.3057 -- 100.0
X Ray Diffraction 3.9247 3.9764 -- 299 5573 0.2115 0.2891 -- 100.0
X Ray Diffraction 3.9764 4.0308 -- 311 5542 0.1948 0.2497 -- 100.0
X Ray Diffraction 4.0308 4.0884 -- 279 5643 0.1812 0.237 -- 100.0
X Ray Diffraction 4.0884 4.1494 -- 316 5542 0.1646 0.234 -- 100.0
X Ray Diffraction 4.1494 4.2142 -- 292 5621 0.1662 0.239 -- 100.0
X Ray Diffraction 4.2142 4.2832 -- 283 5592 0.157 0.2283 -- 100.0
X Ray Diffraction 4.2832 4.357 -- 283 5623 0.141 0.1894 -- 100.0
X Ray Diffraction 4.357 4.4362 -- 319 5549 0.1371 0.207 -- 100.0
X Ray Diffraction 4.4362 4.5215 -- 247 5655 0.1412 0.2083 -- 100.0
X Ray Diffraction 4.5215 4.6137 -- 278 5625 0.1356 0.1922 -- 100.0
X Ray Diffraction 4.6137 4.714 -- 315 5590 0.1193 0.1722 -- 100.0
X Ray Diffraction 4.714 4.8235 -- 287 5617 0.1062 0.1677 -- 100.0
X Ray Diffraction 4.8235 4.9441 -- 285 5640 0.1043 0.1513 -- 100.0
X Ray Diffraction 4.9441 5.0776 -- 276 5628 0.1016 0.1477 -- 100.0
X Ray Diffraction 5.0776 5.2269 -- 316 5627 0.1013 0.1505 -- 100.0
X Ray Diffraction 5.2269 5.3954 -- 292 5636 0.1025 0.1697 -- 100.0
X Ray Diffraction 5.3954 5.588 -- 305 5616 0.0984 0.1557 -- 100.0
X Ray Diffraction 5.588 5.8114 -- 268 5711 0.0938 0.1389 -- 100.0
X Ray Diffraction 5.8114 6.0754 -- 298 5635 0.1022 0.1517 -- 100.0
X Ray Diffraction 6.0754 6.3951 -- 320 5645 0.1014 0.1695 -- 100.0
X Ray Diffraction 6.3951 6.7949 -- 306 5663 0.0986 0.1459 -- 100.0
X Ray Diffraction 6.7949 7.318 -- 298 5696 0.1028 0.1718 -- 100.0
X Ray Diffraction 7.318 8.0517 -- 298 5725 0.1059 0.1573 -- 100.0
X Ray Diffraction 8.0517 9.2104 -- 311 5730 0.1209 0.1643 -- 100.0
X Ray Diffraction 9.2104 11.5802 -- 322 5793 0.1342 0.1756 -- 100.0
X Ray Diffraction 11.5802 49.8584 -- 332 5995 0.1984 0.2172 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 154.619
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 21.31
f_angle_d 2.95
f_plane_restr 0.013
f_chiral_restr 0.138
f_bond_d 0.022
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 19093
Nucleic Acid Atoms 32550
Heterogen Atoms 456
Solvent Atoms 1464

Software

Computing
Computing Package Purpose
XDS Data Collection
XSCALE Data Reduction (intensity integration)
XSCALE Data Reduction (data scaling)
PHENIX (phenix.refine: dev_1119) Structure Solution
PHENIX (phenix.refine: dev_1119) Structure Refinement
Software
Software Name Purpose
phenix refinement
pdb_extract version: 3.11 data extraction
Xscale data reduction