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 = 402.64 α = 90
b = 402.64 β = 90
c = 174.75 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 98.3 0.08 -- -- 3.2 155290 155290 -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 99.5 0.686 -- -- 3.2 15521

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 34.661 -- 1.33 155190 155190 7744 98.2 -- 0.1559 0.1531 0.2083 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 3.6925 -- 277 4708 0.2906 0.3483 -- 96.0
X Ray Diffraction 3.6925 3.7358 -- 256 4930 0.2734 0.3231 -- 100.0
X Ray Diffraction 3.7358 3.7813 -- 292 4890 0.2602 0.3055 -- 100.0
X Ray Diffraction 3.7813 3.8292 -- 210 4940 0.2423 0.3178 -- 99.0
X Ray Diffraction 3.8292 3.8795 -- 264 4964 0.2297 0.2623 -- 100.0
X Ray Diffraction 3.8795 3.9325 -- 268 4914 0.2314 0.2962 -- 100.0
X Ray Diffraction 3.9325 3.9887 -- 247 4965 0.2092 0.2736 -- 100.0
X Ray Diffraction 3.9887 4.0481 -- 280 4874 0.2019 0.2532 -- 99.0
X Ray Diffraction 4.0481 4.1113 -- 285 4916 0.1969 0.2521 -- 99.0
X Ray Diffraction 4.1113 4.1785 -- 241 4966 0.1774 0.2301 -- 99.0
X Ray Diffraction 4.1785 4.2505 -- 253 4932 0.1728 0.2579 -- 99.0
X Ray Diffraction 4.2505 4.3276 -- 260 4896 0.1626 0.2307 -- 99.0
X Ray Diffraction 4.3276 4.4107 -- 275 4934 0.1575 0.2066 -- 99.0
X Ray Diffraction 4.4107 4.5005 -- 292 4906 0.1488 0.2068 -- 99.0
X Ray Diffraction 4.5005 4.5982 -- 255 4946 0.1448 0.2055 -- 99.0
X Ray Diffraction 4.5982 4.7049 -- 238 4938 0.1416 0.2043 -- 99.0
X Ray Diffraction 4.7049 4.8223 -- 227 4992 0.1288 0.1959 -- 99.0
X Ray Diffraction 4.8223 4.9523 -- 280 4912 0.1206 0.1914 -- 99.0
X Ray Diffraction 4.9523 5.0976 -- 256 4945 0.117 0.1736 -- 99.0
X Ray Diffraction 5.0976 5.2616 -- 238 4933 0.1089 0.1643 -- 99.0
X Ray Diffraction 5.2616 5.4489 -- 253 4958 0.1112 0.1703 -- 99.0
X Ray Diffraction 5.4489 5.6662 -- 265 4931 0.113 0.1805 -- 99.0
X Ray Diffraction 5.6662 5.9229 -- 254 4949 0.1099 0.1656 -- 98.0
X Ray Diffraction 5.9229 6.2334 -- 246 4941 0.1146 0.1765 -- 98.0
X Ray Diffraction 6.2334 6.6215 -- 254 4926 0.1288 0.1883 -- 98.0
X Ray Diffraction 6.6215 7.1286 -- 254 4937 0.1293 0.1872 -- 98.0
X Ray Diffraction 7.1286 7.8385 -- 252 4952 0.12 0.1877 -- 97.0
X Ray Diffraction 7.8385 8.9556 -- 259 4900 0.122 0.1603 -- 96.0
X Ray Diffraction 8.9556 11.2192 -- 258 4914 0.1337 0.1686 -- 95.0
X Ray Diffraction 11.2192 34.6624 -- 255 4637 0.2087 0.2492 -- 87.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 168.777
Anisotropic B[1][1] -6.6447
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -6.6447
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 6.993
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 19.908
f_plane_restr 0.009
f_chiral_restr 0.091
f_angle_d 1.62
f_bond_d 0.013
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 19088
Nucleic Acid Atoms 32508
Heterogen Atoms 289
Solvent Atoms 412

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