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 = 403.45 α = 90
b = 403.45 β = 90
c = 173.41 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
3.85 35 97.3 0.075 -- -- 3.0 131031 131031 -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)
3.849 3.99 99.0 0.724 -- -- 3.0 13130

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 3.849 34.93 -- 1.33 130989 130989 6511 97.29 -- 0.1531 0.1501 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 3.849 3.8928 -- 215 4119 0.2681 0.3079 -- 98.0
X Ray Diffraction 3.8928 3.9386 -- 214 4184 0.2688 0.3179 -- 99.0
X Ray Diffraction 3.9386 3.9865 -- 215 4148 0.2587 0.3483 -- 99.0
X Ray Diffraction 3.9865 4.0369 -- 239 4177 0.2476 0.3271 -- 99.0
X Ray Diffraction 4.0369 4.09 -- 237 4111 0.2334 0.3023 -- 99.0
X Ray Diffraction 4.09 4.1459 -- 225 4168 0.2215 0.2897 -- 99.0
X Ray Diffraction 4.1459 4.205 -- 215 4147 0.2073 0.2854 -- 99.0
X Ray Diffraction 4.205 4.2677 -- 180 4220 0.1904 0.2658 -- 99.0
X Ray Diffraction 4.2677 4.3343 -- 247 4170 0.1831 0.2539 -- 98.0
X Ray Diffraction 4.3343 4.4052 -- 221 4121 0.1676 0.2172 -- 99.0
X Ray Diffraction 4.4052 4.481 -- 247 4156 0.165 0.2427 -- 98.0
X Ray Diffraction 4.481 4.5623 -- 220 4146 0.1674 0.2083 -- 98.0
X Ray Diffraction 4.5623 4.6499 -- 212 4149 0.1535 0.2215 -- 98.0
X Ray Diffraction 4.6499 4.7445 -- 191 4170 0.1518 0.2154 -- 98.0
X Ray Diffraction 4.7445 4.8474 -- 207 4197 0.1419 0.2298 -- 98.0
X Ray Diffraction 4.8474 4.9599 -- 233 4151 0.1308 0.1833 -- 98.0
X Ray Diffraction 4.9599 5.0836 -- 221 4150 0.1256 0.1905 -- 98.0
X Ray Diffraction 5.0836 5.2206 -- 195 4191 0.1208 0.1906 -- 98.0
X Ray Diffraction 5.2206 5.3737 -- 208 4156 0.1168 0.1795 -- 98.0
X Ray Diffraction 5.3737 5.5465 -- 224 4140 0.1148 0.1733 -- 98.0
X Ray Diffraction 5.5465 5.7439 -- 217 4162 0.1156 0.2009 -- 98.0
X Ray Diffraction 5.7439 5.9728 -- 205 4189 0.1163 0.1769 -- 97.0
X Ray Diffraction 5.9728 6.2431 -- 205 4151 0.118 0.1852 -- 97.0
X Ray Diffraction 6.2431 6.5702 -- 206 4180 0.1209 0.1791 -- 97.0
X Ray Diffraction 6.5702 6.9788 -- 212 4155 0.114 0.19 -- 97.0
X Ray Diffraction 6.9788 7.5127 -- 236 4138 0.1149 0.1824 -- 96.0
X Ray Diffraction 7.5127 8.2597 -- 195 4172 0.1179 0.1864 -- 96.0
X Ray Diffraction 8.2597 9.4342 -- 237 4031 0.1209 0.1709 -- 94.0
X Ray Diffraction 9.4342 11.8093 -- 213 4163 0.1245 0.1755 -- 94.0
X Ray Diffraction 11.8093 34.9312 -- 219 3966 0.2067 0.2511 -- 87.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 198.966
Anisotropic B[1][1] -13.4379
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -13.4379
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 16.5628
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 19.867
f_plane_restr 0.009
f_chiral_restr 0.086
f_angle_d 1.52
f_bond_d 0.012
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 19088
Nucleic Acid Atoms 32510
Heterogen Atoms 289
Solvent Atoms 410

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