X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 6.5
Temperature 296.0
Details 29.2% PEG3350, 0.1M NaF, 0.1M Bis-Tris propane, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 296K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 127.98 α = 90
b = 128.48 β = 90
c = 225.93 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
2 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 210r -- 2009-12-16
CCD ADSC QUANTUM 210r -- 2009-12-16
Diffraction Radiation
Monochromator Protocol
Double Crystal Si(111) single wavelength
Double Crystal Si(111) single wavelength
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1.0000 PHOTON FACTORY AR-NW12A
SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 0.97919 PHOTON FACTORY AR-NW12A

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
2.17 37.12 99.7 0.09 -- -- 7.4 195452 195452 -3.0 -3.0 29.349
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)
2.17 2.23 97.1 0.535 -- 3.7 7.2 13905

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
MOLECULAR REPLACEMENT and SAD 2.172 34.042 -- 1.32 -- 194627 9799 98.96 0.1685 0.1685 0.1665 0.2108 RANDOM
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 2.1731 2.2105 -- 943 17502 0.2303 0.2669 -- 92.0
X Ray Diffraction 2.2105 2.2507 -- 946 17895 0.2263 0.2756 -- 95.0
X Ray Diffraction 2.2507 2.294 -- 943 18031 0.2226 0.2548 -- 95.0
X Ray Diffraction 2.294 2.3408 -- 981 17847 0.2117 0.2573 -- 95.0
X Ray Diffraction 2.3408 2.3917 -- 986 17861 0.2078 0.2546 -- 95.0
X Ray Diffraction 2.3917 2.4473 -- 910 18057 0.2066 0.2511 -- 95.0
X Ray Diffraction 2.4473 2.5084 -- 962 17943 0.2039 0.253 -- 95.0
X Ray Diffraction 2.5084 2.5762 -- 878 18006 0.2011 0.2475 -- 95.0
X Ray Diffraction 2.5762 2.652 -- 973 17938 0.1916 0.2361 -- 95.0
X Ray Diffraction 2.652 2.7375 -- 1008 17957 0.1891 0.2422 -- 95.0
X Ray Diffraction 2.7375 2.8352 -- 1041 17894 0.1819 0.2382 -- 94.0
X Ray Diffraction 2.8352 2.9486 -- 876 17998 0.1774 0.2262 -- 95.0
X Ray Diffraction 2.9486 3.0827 -- 941 17963 0.1699 0.2269 -- 95.0
X Ray Diffraction 3.0827 3.245 -- 959 17949 0.1625 0.221 -- 95.0
X Ray Diffraction 3.245 3.4479 -- 941 18005 0.1543 0.2174 -- 95.0
X Ray Diffraction 3.4479 3.7136 -- 1004 17838 0.1397 0.1867 -- 94.0
X Ray Diffraction 3.7136 4.0863 -- 989 17722 0.1287 0.1717 -- 94.0
X Ray Diffraction 4.0863 4.6752 -- 928 17635 0.1164 0.1535 -- 93.0
X Ray Diffraction 4.6752 5.8814 -- 905 17482 0.144 0.1697 -- 92.0
X Ray Diffraction 5.8814 28.0517 -- 835 16955 0.1731 0.2014 -- 90.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 32.7787
Anisotropic B[1][1] -0.5525
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.2784
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.8309
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 12.97
f_plane_restr 0.003
f_chiral_restr 0.051
f_angle_d 0.738
f_bond_d 0.003
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 26189
Nucleic Acid Atoms 0
Heterogen Atoms 87
Solvent Atoms 1795

Software

Computing
Computing Package Purpose
UGUI Data Collection
XDS Data Reduction (intensity integration)
XDS Data Reduction (data scaling)
PHASER Structure Solution
PHENIX (phenix.refine: dev_934) Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine: dev_934) refinement
PHASER model building
UGUI data collection