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 = 400.95 α = 90
b = 400.95 β = 90
c = 176.68 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 -- 2008-12-03
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
3.97 50 100.0 0.253 -- -- 7.3 123861 123861 -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)
3.969 4.04 100.0 0.992 -- -- 6.7 6102

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 3.969 49.732 -- 1.34 123736 123736 6187 99.94 -- 0.1561 0.1531 0.2124 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 3.969 4.0144 -- 221 3867 0.2245 0.3026 -- 100.0
X Ray Diffraction 4.0144 4.0616 -- 226 3825 0.2142 0.3067 -- 100.0
X Ray Diffraction 4.0616 4.1111 -- 215 3862 0.2053 0.2691 -- 100.0
X Ray Diffraction 4.1111 4.1632 -- 187 3866 0.182 0.2414 -- 100.0
X Ray Diffraction 4.1632 4.2179 -- 201 3913 0.1735 0.2509 -- 100.0
X Ray Diffraction 4.2179 4.2757 -- 202 3865 0.1678 0.248 -- 100.0
X Ray Diffraction 4.2757 4.3367 -- 213 3887 0.1729 0.2522 -- 100.0
X Ray Diffraction 4.3367 4.4014 -- 227 3852 0.1744 0.2364 -- 100.0
X Ray Diffraction 4.4014 4.4701 -- 212 3855 0.151 0.235 -- 100.0
X Ray Diffraction 4.4701 4.5434 -- 213 3895 0.1575 0.2215 -- 100.0
X Ray Diffraction 4.5434 4.6217 -- 191 3888 0.1482 0.223 -- 100.0
X Ray Diffraction 4.6217 4.7056 -- 185 3892 0.142 0.1844 -- 100.0
X Ray Diffraction 4.7056 4.7961 -- 193 3910 0.1401 0.2231 -- 100.0
X Ray Diffraction 4.7961 4.8939 -- 192 3915 0.1388 0.2201 -- 100.0
X Ray Diffraction 4.8939 5.0002 -- 219 3868 0.1265 0.1951 -- 100.0
X Ray Diffraction 5.0002 5.1164 -- 192 3908 0.1276 0.1865 -- 100.0
X Ray Diffraction 5.1164 5.2442 -- 202 3914 0.1239 0.1894 -- 100.0
X Ray Diffraction 5.2442 5.3859 -- 199 3911 0.1161 0.1724 -- 100.0
X Ray Diffraction 5.3859 5.5441 -- 211 3924 0.1094 0.1859 -- 100.0
X Ray Diffraction 5.5441 5.7228 -- 209 3891 0.1114 0.1746 -- 100.0
X Ray Diffraction 5.7228 5.9271 -- 195 3936 0.1155 0.1903 -- 100.0
X Ray Diffraction 5.9271 6.164 -- 197 3930 0.1166 0.1907 -- 100.0
X Ray Diffraction 6.164 6.4439 -- 192 3947 0.1169 0.1673 -- 100.0
X Ray Diffraction 6.4439 6.7829 -- 219 3926 0.1186 0.1969 -- 100.0
X Ray Diffraction 6.7829 7.2067 -- 201 3938 0.1109 0.1777 -- 100.0
X Ray Diffraction 7.2067 7.7612 -- 202 3986 0.1178 0.1643 -- 100.0
X Ray Diffraction 7.7612 8.5387 -- 209 3976 0.1301 0.1848 -- 100.0
X Ray Diffraction 8.5387 9.7661 -- 230 3988 0.1461 0.205 -- 100.0
X Ray Diffraction 9.7661 12.2736 -- 204 4023 0.1621 0.1983 -- 99.0
X Ray Diffraction 12.2736 49.7357 -- 228 4191 0.2594 0.2554 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 101.162
Anisotropic B[1][1] -12.2147
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -12.2147
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 2.7328
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 26.098
f_plane_restr 0.008
f_chiral_restr 0.083
f_angle_d 1.527
f_bond_d 0.013
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 19152
Nucleic Acid Atoms 32880
Heterogen Atoms 1115
Solvent Atoms 498

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