X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Microbatch Crystallization Under Oil
pH 8
Temperature 291.0
Details 1.11M sodium phosphate, 0.1M Tris-HCl, pH 8.0, Microbatch crystallization under oil, temperature 291K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 87.77 α = 90
b = 87.77 β = 90
c = 76.08 γ = 120
Symmetry
Space Group P 61 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315 -- 2012-12-19
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 24-ID-E 0.97923 APS 24-ID-E

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
2.53 50 99.2 0.054 -- -- 13.6 10991 10905 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)
2.53 2.65 99.2 0.0127 -- 2.2 14.3 1422

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
SAD 2.53 33.999 -- 1.35 -- 10899 485 99.45 -- 0.243 0.24 0.292 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 2.5711 2.5297 -- 154 3459 0.356 0.358 -- 99.0
X Ray Diffraction 2.895 3.647 -- 179 3487 0.265 0.316 -- 100.0
X Ray Diffraction 3.647 34.002 -- 152 3468 0.215 0.27 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 91.813
Anisotropic B[1][1] 1.604
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 1.604
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -3.207
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 18.884
f_plane_restr 0.006
f_chiral_restr 0.082
f_angle_d 1.399
f_bond_d 0.01
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 902
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 17

Software

Computing
Computing Package Purpose
ADSC Quantum Data Collection
XDS Data Reduction (intensity integration)
XScale Data Reduction (data scaling)
phenix.autosol Structure Solution
PHENIX (phenix.refine: 1.7.2_869) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.100 data extraction
phenix refinement