X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

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

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 402.52 α = 90
b = 402.52 β = 90
c = 173.98 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 -- 2010-11-07
Diffraction Radiation
Monochromator Protocol
Kohzu HLD8-24 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
3.65 35 95.8 0.08 -- -- 3.0 150484 150484 -3.0 -3.0 --
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)
3.65 3.78 97.6 0.519 -- -- 2.8 15146

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 3.651 34.561 -- 1.33 150379 150379 7501 95.63 -- 0.1587 0.1556 0.216 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 3.651 3.6928 -- 272 4606 0.2684 0.33 -- 93.0
X Ray Diffraction 3.6928 3.7362 -- 243 4752 0.2528 0.3417 -- 98.0
X Ray Diffraction 3.7362 3.7817 -- 270 4829 0.2394 0.2845 -- 98.0
X Ray Diffraction 3.7817 3.8295 -- 220 4823 0.2332 0.2932 -- 97.0
X Ray Diffraction 3.8295 3.8798 -- 257 4821 0.2246 0.2742 -- 98.0
X Ray Diffraction 3.8798 3.9329 -- 253 4740 0.2229 0.3073 -- 97.0
X Ray Diffraction 3.9329 3.989 -- 254 4854 0.2132 0.2806 -- 97.0
X Ray Diffraction 3.989 4.0485 -- 268 4797 0.2048 0.2734 -- 97.0
X Ray Diffraction 4.0485 4.1116 -- 285 4742 0.1943 0.2656 -- 97.0
X Ray Diffraction 4.1116 4.1789 -- 230 4817 0.1798 0.2359 -- 97.0
X Ray Diffraction 4.1789 4.2509 -- 232 4825 0.1666 0.2494 -- 97.0
X Ray Diffraction 4.2509 4.328 -- 256 4792 0.1604 0.2124 -- 97.0
X Ray Diffraction 4.328 4.4111 -- 260 4750 0.1633 0.2186 -- 97.0
X Ray Diffraction 4.4111 4.501 -- 286 4757 0.1614 0.2355 -- 97.0
X Ray Diffraction 4.501 4.5986 -- 246 4786 0.1537 0.2186 -- 96.0
X Ray Diffraction 4.5986 4.7053 -- 228 4839 0.1423 0.1983 -- 97.0
X Ray Diffraction 4.7053 4.8227 -- 232 4795 0.1352 0.2146 -- 97.0
X Ray Diffraction 4.8227 4.9527 -- 272 4741 0.1234 0.1807 -- 96.0
X Ray Diffraction 4.9527 5.098 -- 242 4787 0.1218 0.1881 -- 96.0
X Ray Diffraction 5.098 5.262 -- 233 4789 0.1216 0.1935 -- 96.0
X Ray Diffraction 5.262 5.4494 -- 246 4790 0.1166 0.1769 -- 96.0
X Ray Diffraction 5.4494 5.6667 -- 247 4761 0.1163 0.1817 -- 96.0
X Ray Diffraction 5.6667 5.9234 -- 247 4775 0.1155 0.1667 -- 95.0
X Ray Diffraction 5.9234 6.2339 -- 235 4762 0.1201 0.1902 -- 95.0
X Ray Diffraction 6.2339 6.622 -- 248 4753 0.1292 0.1996 -- 95.0
X Ray Diffraction 6.622 7.1291 -- 243 4724 0.1267 0.1833 -- 94.0
X Ray Diffraction 7.1291 7.839 -- 241 4760 0.1312 0.2082 -- 94.0
X Ray Diffraction 7.839 8.956 -- 255 4698 0.1351 0.1789 -- 93.0
X Ray Diffraction 8.956 11.2192 -- 253 4701 0.1419 0.1906 -- 92.0
X Ray Diffraction 11.2192 34.5625 -- 247 4512 0.2042 0.247 -- 85.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 172.503
Anisotropic B[1][1] -8.3745
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -8.3745
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 6.7012
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 20.366
f_plane_restr 0.01
f_chiral_restr 0.094
f_angle_d 1.698
f_bond_d 0.014
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 19088
Nucleic Acid Atoms 32507
Heterogen Atoms 309
Solvent Atoms 385

Software

Computing
Computing Package Purpose
HKL-2000 Data Collection
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
PHENIX (phenix.refine: dev_978) Structure Solution
PHENIX (phenix.refine: dev_978) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.10 data extraction
phenix refinement
SCALEPACK data reduction
DENZO data collection