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 = 401.83 α = 90
b = 401.83 β = 90
c = 175.89 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
3.6 35 99.4 0.086 -- -- 3.3 163923 163923 -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)
3.6 3.73 99.9 0.789 -- -- 3.3 16240

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 3.602 34.457 -- 1.34 163849 163849 8182 99.36 0.1651 0.1651 0.1628 0.2089 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 3.602 3.6429 -- 251 5127 0.2824 0.329 -- 100.0
X Ray Diffraction 3.6429 3.6857 -- 296 5153 0.2558 0.2862 -- 100.0
X Ray Diffraction 3.6857 3.7306 -- 290 5110 0.2416 0.2983 -- 100.0
X Ray Diffraction 3.7306 3.7778 -- 295 5123 0.2362 0.2933 -- 100.0
X Ray Diffraction 3.7778 3.8274 -- 223 5238 0.2256 0.2891 -- 100.0
X Ray Diffraction 3.8274 3.8798 -- 264 5189 0.2047 0.2668 -- 100.0
X Ray Diffraction 3.8798 3.9352 -- 301 5105 0.1971 0.2368 -- 100.0
X Ray Diffraction 3.9352 3.9938 -- 251 5229 0.1888 0.2285 -- 100.0
X Ray Diffraction 3.9938 4.0561 -- 289 5131 0.1895 0.2379 -- 100.0
X Ray Diffraction 4.0561 4.1225 -- 296 5150 0.1722 0.2271 -- 100.0
X Ray Diffraction 4.1225 4.1935 -- 246 5183 0.164 0.2327 -- 100.0
X Ray Diffraction 4.1935 4.2696 -- 270 5166 0.1574 0.2162 -- 100.0
X Ray Diffraction 4.2696 4.3516 -- 287 5137 0.147 0.2026 -- 100.0
X Ray Diffraction 4.3516 4.4402 -- 271 5165 0.1435 0.1859 -- 100.0
X Ray Diffraction 4.4402 4.5366 -- 308 5141 0.1403 0.187 -- 100.0
X Ray Diffraction 4.5366 4.6418 -- 258 5203 0.1297 0.1719 -- 100.0
X Ray Diffraction 4.6418 4.7576 -- 248 5212 0.13 0.1836 -- 100.0
X Ray Diffraction 4.7576 4.8859 -- 260 5187 0.1319 0.1968 -- 100.0
X Ray Diffraction 4.8859 5.0293 -- 291 5200 0.1298 0.1889 -- 100.0
X Ray Diffraction 5.0293 5.1911 -- 258 5174 0.1228 0.1603 -- 99.0
X Ray Diffraction 5.1911 5.376 -- 262 5188 0.1223 0.1713 -- 100.0
X Ray Diffraction 5.376 5.5903 -- 283 5224 0.1239 0.18 -- 100.0
X Ray Diffraction 5.5903 5.8436 -- 278 5235 0.1246 0.1795 -- 100.0
X Ray Diffraction 5.8436 6.15 -- 249 5247 0.1272 0.1827 -- 100.0
X Ray Diffraction 6.15 6.5329 -- 264 5272 0.1292 0.1731 -- 100.0
X Ray Diffraction 6.5329 7.0334 -- 275 5246 0.1315 0.172 -- 100.0
X Ray Diffraction 7.0334 7.7339 -- 277 5247 0.136 0.178 -- 99.0
X Ray Diffraction 7.7339 8.8365 -- 277 5261 0.1482 0.2017 -- 99.0
X Ray Diffraction 8.8365 11.0714 -- 279 5248 0.1762 0.1989 -- 98.0
X Ray Diffraction 11.0714 34.4583 -- 285 5176 0.2335 0.2601 -- 93.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 133.258
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 17.259
f_plane_restr 0.006
f_chiral_restr 0.068
f_angle_d 1.425
f_bond_d 0.01
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 19153
Nucleic Acid Atoms 32504
Heterogen Atoms 183
Solvent Atoms 48

Software

Computing
Computing Package Purpose
HKL-2000 Data Collection
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
PHENIX Structure Solution
PHENIX (phenix.refine: dev_1119) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
phenix refinement
SCALEPACK data reduction
DENZO data collection