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_chiral_restr 0.059
f_dihedral_angle_d 18.074
f_bond_d 0.006
f_angle_d 1.044
f_plane_restr 0.005
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

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