X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 5.2
Temperature 298.0
Details 0.49M sodium citrate, 0.1M citric acid, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 96.13 α = 90
b = 96.13 β = 90
c = 151.33 γ = 120
Symmetry
Space Group P 63

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
PIXEL DECTRIS PILATUS 6M-F -- 2012-11-08
Diffraction Radiation
Monochromator Protocol
Cryo-cooled double crystal SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 24-ID-C 0.979 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 36.47 89.9 -- -- -- -- 9319 9319 0.0 0.0 --
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 17.6 -- -- -- -- --

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
-- 3.603 36.47 -- 1.4 -- 8343 849 90.58 -- 0.2737 0.2704 0.302 --
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 3.6031 3.8286 -- 72 606 0.361 0.3898 -- 44.0
X Ray Diffraction 3.8286 4.1238 -- 151 1367 0.3022 0.3124 -- 100.0
X Ray Diffraction 4.1238 4.5381 -- 136 1397 0.2504 0.3121 -- 100.0
X Ray Diffraction 4.5381 5.1932 -- 171 1357 0.2547 0.2698 -- 100.0
X Ray Diffraction 5.1932 6.5367 -- 156 1374 0.2847 0.3274 -- 100.0
X Ray Diffraction 6.5367 36.4716 -- 163 1393 0.2462 0.2801 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Anisotropic B[1][1] 2.3035
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 2.3035
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -4.607
RMS Deviations
Key Refinement Restraint Deviation
f_angle_d 1.196
f_plane_restr 0.004
f_bond_d 0.011
f_dihedral_angle_d 20.018
f_chiral_restr 0.078
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3133
Nucleic Acid Atoms 0
Heterogen Atoms 6
Solvent Atoms 0

Software

Software
Software Name Purpose
HKL-2000 data collection
PHENIX model building version: (Autosol)
PHENIX refinement version: (phenix.refine: 1.7.3_928)
HKL-2000 data reduction
HKL-2000 data scaling
PHENIX phasing version: (Autosol)