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 = 403.74 α = 90
b = 403.74 β = 90
c = 174.34 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
3.49 50 99.1 0.077 -- -- -- 179519 179519 -3.0 -3.0 116.443
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)
3.49 3.7 96.4 0.763 -- 1.71 -- --

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 3.492 49.528 -- 1.99 179494 179494 9024 99.1 -- 0.1692 0.167 0.2116 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 3.4917 3.5314 -- 246 4692 0.3065 0.3603 -- 83.0
X Ray Diffraction 3.5314 3.5729 -- 299 5680 0.2797 0.3223 -- 100.0
X Ray Diffraction 3.5729 3.6165 -- 305 5614 0.2653 0.3199 -- 100.0
X Ray Diffraction 3.6165 3.6622 -- 328 5646 0.2535 0.2956 -- 100.0
X Ray Diffraction 3.6622 3.7104 -- 289 5713 0.2405 0.2745 -- 100.0
X Ray Diffraction 3.7104 3.7612 -- 326 5626 0.2275 0.263 -- 100.0
X Ray Diffraction 3.7612 3.8149 -- 290 5689 0.2118 0.2673 -- 100.0
X Ray Diffraction 3.8149 3.8718 -- 334 5655 0.2011 0.2715 -- 100.0
X Ray Diffraction 3.8718 3.9323 -- 272 5709 0.2043 0.251 -- 100.0
X Ray Diffraction 3.9323 3.9968 -- 309 5658 0.2045 0.2532 -- 100.0
X Ray Diffraction 3.9968 4.0657 -- 279 5700 0.1933 0.2526 -- 100.0
X Ray Diffraction 4.0657 4.1396 -- 297 5693 0.182 0.2402 -- 100.0
X Ray Diffraction 4.1396 4.2191 -- 303 5675 0.1691 0.238 -- 100.0
X Ray Diffraction 4.2191 4.3052 -- 292 5695 0.1688 0.2121 -- 100.0
X Ray Diffraction 4.3052 4.3988 -- 304 5720 0.1599 0.2233 -- 100.0
X Ray Diffraction 4.3988 4.501 -- 303 5686 0.1559 0.1917 -- 100.0
X Ray Diffraction 4.501 4.6135 -- 270 5731 0.1447 0.1937 -- 100.0
X Ray Diffraction 4.6135 4.7381 -- 296 5722 0.1397 0.2013 -- 100.0
X Ray Diffraction 4.7381 4.8774 -- 301 5689 0.1376 0.1803 -- 100.0
X Ray Diffraction 4.8774 5.0347 -- 264 5757 0.1337 0.191 -- 100.0
X Ray Diffraction 5.0347 5.2145 -- 297 5707 0.1365 0.1838 -- 100.0
X Ray Diffraction 5.2145 5.423 -- 330 5722 0.1324 0.1859 -- 100.0
X Ray Diffraction 5.423 5.6695 -- 286 5748 0.1317 0.1881 -- 100.0
X Ray Diffraction 5.6695 5.9679 -- 325 5733 0.134 0.1956 -- 100.0
X Ray Diffraction 5.9679 6.3411 -- 303 5749 0.1362 0.2052 -- 100.0
X Ray Diffraction 6.3411 6.8296 -- 288 5799 0.1383 0.1834 -- 100.0
X Ray Diffraction 6.8296 7.5148 -- 318 5784 0.1425 0.1889 -- 100.0
X Ray Diffraction 7.5148 8.5973 -- 312 5797 0.1485 0.1941 -- 99.0
X Ray Diffraction 8.5973 10.813 -- 324 5811 0.159 0.2081 -- 99.0
X Ray Diffraction 10.813 49.5326 -- 334 5870 0.1953 0.1922 -- 96.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 168.292
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 18.074
f_plane_restr 0.005
f_chiral_restr 0.059
f_angle_d 1.044
f_bond_d 0.006
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 19089
Nucleic Acid Atoms 32507
Heterogen Atoms 308
Solvent Atoms 275

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