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 = 402.08 α = 90
b = 402.08 β = 90
c = 174.61 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
CCD ADSC QUANTUM 315 -- 2011-08-03
Diffraction Radiation
Monochromator Protocol
Kohzu HLD8-24 Monochromator SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 24-ID-C 0.98 APS 24-ID-C

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
3.69 50 98.4 0.081 -- -- -- 150281 150281 -3.0 -3.0 132.8
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)
3.69 3.91 96.5 0.806 -- 1.79 -- --

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 3.692 48.299 -- 1.99 150242 150242 7538 98.48 -- 0.1593 0.1564 0.214 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 3.6917 3.7336 -- 218 3979 0.2896 0.3258 -- 84.0
X Ray Diffraction 3.7336 3.7775 -- 259 4774 0.2579 0.3297 -- 100.0
X Ray Diffraction 3.7775 3.8236 -- 278 4718 0.2459 0.3004 -- 100.0
X Ray Diffraction 3.8236 3.872 -- 284 4762 0.235 0.2992 -- 100.0
X Ray Diffraction 3.872 3.9229 -- 209 4807 0.237 0.2637 -- 100.0
X Ray Diffraction 3.9229 3.9766 -- 257 4799 0.2206 0.2799 -- 100.0
X Ray Diffraction 3.9766 4.0334 -- 248 4769 0.2136 0.2872 -- 100.0
X Ray Diffraction 4.0334 4.0935 -- 233 4798 0.2157 0.319 -- 100.0
X Ray Diffraction 4.0935 4.1575 -- 253 4797 0.1983 0.2821 -- 100.0
X Ray Diffraction 4.1575 4.2256 -- 264 4753 0.1903 0.2552 -- 100.0
X Ray Diffraction 4.2256 4.2984 -- 235 4787 0.1767 0.2393 -- 100.0
X Ray Diffraction 4.2984 4.3765 -- 256 4786 0.171 0.2499 -- 100.0
X Ray Diffraction 4.3765 4.4607 -- 268 4743 0.164 0.2226 -- 100.0
X Ray Diffraction 4.4607 4.5516 -- 215 4848 0.1503 0.2157 -- 100.0
X Ray Diffraction 4.5516 4.6505 -- 246 4779 0.1479 0.2228 -- 100.0
X Ray Diffraction 4.6505 4.7586 -- 251 4805 0.138 0.2162 -- 100.0
X Ray Diffraction 4.7586 4.8775 -- 242 4774 0.1349 0.1929 -- 99.0
X Ray Diffraction 4.8775 5.0093 -- 223 4802 0.1322 0.195 -- 99.0
X Ray Diffraction 5.0093 5.1565 -- 262 4795 0.1281 0.1963 -- 99.0
X Ray Diffraction 5.1565 5.3227 -- 256 4762 0.1267 0.1815 -- 99.0
X Ray Diffraction 5.3227 5.5127 -- 257 4770 0.1253 0.1955 -- 99.0
X Ray Diffraction 5.5127 5.7331 -- 238 4783 0.1214 0.1927 -- 99.0
X Ray Diffraction 5.7331 5.9936 -- 290 4758 0.1183 0.1962 -- 99.0
X Ray Diffraction 5.9936 6.3089 -- 242 4763 0.1204 0.1911 -- 98.0
X Ray Diffraction 6.3089 6.7032 -- 246 4812 0.1216 0.1759 -- 98.0
X Ray Diffraction 6.7032 7.2192 -- 237 4791 0.1191 0.1784 -- 98.0
X Ray Diffraction 7.2192 7.9429 -- 256 4802 0.1197 0.1884 -- 98.0
X Ray Diffraction 7.9429 9.0856 -- 274 4717 0.1287 0.1753 -- 97.0
X Ray Diffraction 9.0856 11.4218 -- 272 4823 0.141 0.2021 -- 97.0
X Ray Diffraction 11.4218 48.3032 -- 269 4848 0.1969 0.2146 -- 94.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 183.528
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 20.048
f_plane_restr 0.008
f_chiral_restr 0.088
f_angle_d 1.796
f_bond_d 0.012
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 19089
Nucleic Acid Atoms 32507
Heterogen Atoms 276
Solvent Atoms 272

Software

Computing
Computing Package Purpose
ADSC Quantum 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
pdb_extract version: 3.11 data extraction
phenix refinement
Xscale data reduction