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 = 402.11 α = 90
b = 402.11 β = 90
c = 174 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 HLD8-24r 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
3.85 35 97.6 0.071 -- -- 3.2 130659 130659 -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)
3.85 3.99 99.5 0.817 -- -- 3.2 13123

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 3.853 34.823 -- 1.34 130643 130643 6509 97.65 -- 0.1504 0.1475 0.2059 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 3.853 3.8969 -- 229 4098 0.2729 0.299 -- 98.0
X Ray Diffraction 3.8969 3.9426 -- 209 4191 0.2539 0.329 -- 99.0
X Ray Diffraction 3.9426 3.9906 -- 212 4137 0.2504 0.3011 -- 99.0
X Ray Diffraction 3.9906 4.0411 -- 237 4177 0.2441 0.3193 -- 100.0
X Ray Diffraction 4.0411 4.0942 -- 247 4147 0.2376 0.3073 -- 100.0
X Ray Diffraction 4.0942 4.1502 -- 208 4164 0.215 0.2857 -- 99.0
X Ray Diffraction 4.1502 4.2094 -- 225 4169 0.2013 0.2971 -- 100.0
X Ray Diffraction 4.2094 4.2721 -- 191 4164 0.197 0.257 -- 99.0
X Ray Diffraction 4.2721 4.3387 -- 249 4179 0.1873 0.256 -- 99.0
X Ray Diffraction 4.3387 4.4097 -- 219 4150 0.1796 0.2305 -- 99.0
X Ray Diffraction 4.4097 4.4856 -- 248 4126 0.1591 0.2116 -- 99.0
X Ray Diffraction 4.4856 4.567 -- 218 4209 0.1522 0.1922 -- 99.0
X Ray Diffraction 4.567 4.6546 -- 203 4149 0.1414 0.1884 -- 99.0
X Ray Diffraction 4.6546 4.7494 -- 198 4181 0.137 0.2163 -- 99.0
X Ray Diffraction 4.7494 4.8524 -- 208 4174 0.1332 0.1909 -- 99.0
X Ray Diffraction 4.8524 4.965 -- 233 4150 0.1184 0.1703 -- 99.0
X Ray Diffraction 4.965 5.0888 -- 215 4173 0.1153 0.1759 -- 99.0
X Ray Diffraction 5.0888 5.226 -- 199 4139 0.1084 0.179 -- 98.0
X Ray Diffraction 5.226 5.3792 -- 214 4160 0.1091 0.1764 -- 98.0
X Ray Diffraction 5.3792 5.5522 -- 223 4167 0.1078 0.1678 -- 98.0
X Ray Diffraction 5.5522 5.7497 -- 221 4113 0.1105 0.1869 -- 98.0
X Ray Diffraction 5.7497 5.9789 -- 196 4165 0.1144 0.1712 -- 98.0
X Ray Diffraction 5.9789 6.2495 -- 202 4129 0.1186 0.1902 -- 97.0
X Ray Diffraction 6.2495 6.5769 -- 212 4131 0.1144 0.1669 -- 97.0
X Ray Diffraction 6.5769 6.9859 -- 205 4138 0.1076 0.1877 -- 96.0
X Ray Diffraction 6.9859 7.5202 -- 235 4091 0.11 0.1777 -- 96.0
X Ray Diffraction 7.5202 8.2678 -- 193 4140 0.117 0.181 -- 95.0
X Ray Diffraction 8.2678 9.4433 -- 241 4051 0.1246 0.183 -- 94.0
X Ray Diffraction 9.4433 11.8198 -- 213 4139 0.1332 0.1886 -- 94.0
X Ray Diffraction 11.8198 34.824 -- 206 3833 0.2101 0.2365 -- 85.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 196.63
Anisotropic B[1][1] -10.2483
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -10.2483
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 10.0849
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 19.524
f_plane_restr 0.008
f_chiral_restr 0.082
f_angle_d 1.428
f_bond_d 0.011
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 19088
Nucleic Acid Atoms 32510
Heterogen Atoms 279
Solvent Atoms 439

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