X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 5.7
Temperature 293.0
Details 11 - 26 % (w/v) PEG 3350 and 0.1 M sodium citrate buffer, pH 5.7, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 72.8 α = 90
b = 140.55 β = 90
c = 146.95 γ = 90
Symmetry
Space Group I 2 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 173
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315r -- 2008-11-11
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 24-ID-C 0.97949 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
1.85 50 99.9 0.059 -- -- 7.3 -- 64199 -- -- --
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)
1.85 1.92 100.0 0.417 -- -- 7.3 6341

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 1.851 40.64 -- 1.33 -- 64135 3233 99.48 -- 0.194 0.1924 0.2245 --
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 1.851 1.8787 -- 113 2478 0.2299 0.2962 -- 93.0
X Ray Diffraction 1.8787 1.908 -- 149 2647 0.2114 0.2433 -- 100.0
X Ray Diffraction 1.908 1.9393 -- 159 2571 0.1976 0.2797 -- 100.0
X Ray Diffraction 1.9393 1.9727 -- 143 2636 0.2021 0.231 -- 100.0
X Ray Diffraction 1.9727 2.0086 -- 149 2619 0.1992 0.2393 -- 100.0
X Ray Diffraction 2.0086 2.0473 -- 152 2629 0.1934 0.2085 -- 100.0
X Ray Diffraction 2.0473 2.089 -- 150 2625 0.1935 0.214 -- 100.0
X Ray Diffraction 2.089 2.1345 -- 142 2638 0.1975 0.2261 -- 100.0
X Ray Diffraction 2.1345 2.1841 -- 143 2610 0.1893 0.2562 -- 100.0
X Ray Diffraction 2.1841 2.2387 -- 120 2665 0.1905 0.2199 -- 100.0
X Ray Diffraction 2.2387 2.2993 -- 131 2678 0.1996 0.2439 -- 100.0
X Ray Diffraction 2.2993 2.3669 -- 147 2623 0.1896 0.1793 -- 100.0
X Ray Diffraction 2.3669 2.4433 -- 149 2635 0.1914 0.2352 -- 100.0
X Ray Diffraction 2.4433 2.5306 -- 151 2635 0.1956 0.2352 -- 100.0
X Ray Diffraction 2.5306 2.6319 -- 131 2677 0.1986 0.2407 -- 100.0
X Ray Diffraction 2.6319 2.7517 -- 124 2649 0.2022 0.2095 -- 100.0
X Ray Diffraction 2.7517 2.8967 -- 146 2646 0.2021 0.2126 -- 100.0
X Ray Diffraction 2.8967 3.0781 -- 142 2677 0.2149 0.2594 -- 100.0
X Ray Diffraction 3.0781 3.3157 -- 143 2668 0.2089 0.2426 -- 100.0
X Ray Diffraction 3.3157 3.6492 -- 135 2692 0.1995 0.2768 -- 100.0
X Ray Diffraction 3.6492 4.1768 -- 139 2697 0.1732 0.1978 -- 100.0
X Ray Diffraction 4.1768 5.2605 -- 144 2719 0.1564 0.1766 -- 100.0
X Ray Diffraction 5.2605 40.6497 -- 131 2788 0.201 0.2291 -- 97.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 37.2924
RMS Deviations
Key Refinement Restraint Deviation
f_angle_d 1.079
f_bond_d 0.007
f_dihedral_angle_d 16.504
f_plane_restr 0.004
f_chiral_restr 0.069
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3709
Nucleic Acid Atoms 0
Heterogen Atoms 87
Solvent Atoms 258

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
PHENIX refinement version: 1.8_1069
PDB_EXTRACT data extraction version: 3.11
HKL-2000 data reduction