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_chiral_restr 0.088
f_plane_restr 0.008
f_bond_d 0.012
f_dihedral_angle_d 20.048
f_angle_d 1.796
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

Software
Software Name Purpose
XSCALE data scaling
PHENIX refinement version: dev_1119
PDB_EXTRACT data extraction version: 3.11
ADSC data collection version: Quantum
PHENIX phasing version: dev_1119