X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.5
Temperature 298.0
Details crystals grown in 0.1M Amm Sulfate, 0.1M cacodylate pH 6.5, 7.5% Peg8K, 5mM MgCl2, 5mM MnCl2, 5mM DTT Ligand dissolved in DMSO at 375mM and added to cryo buffer for overnight soak (5%)

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 72.6 α = 90
b = 72.6 β = 90
c = 65.72 γ = 120
Symmetry
Space Group P 31 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD RAYONIX MX-225 -- 2012-04-12
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 21-ID-F 1.0781 APS 21-ID-F

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
1.8 50 99.9 0.036 -- 46.091 7.3 -- 18964 -- -- 36.54
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)
1.8 1.86 100.0 0.654 -- -- 7.3 1870

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
-- 1.88 17.73 -- 0.0 -- 16628 527 99.93 -- 0.1958 0.1946 0.2353 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 1.88 2.01 -- 90 2878 0.222 0.2908 -- 99.93
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 41.97
Anisotropic B[1][1] -2.8747
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -2.8747
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 5.7494
RMS Deviations
Key Refinement Restraint Deviation
t_omega_torsion 3.23
t_bond_d 0.01
t_other_torsion 2.79
t_angle_deg 0.93
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.219
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1067
Nucleic Acid Atoms 0
Heterogen Atoms 64
Solvent Atoms 120

Software

Software
Software Name Purpose
HKL-2000 data collection
SCALEPACK data scaling
BUSTER refinement version: 2.11.2
PDB_EXTRACT data extraction version: 3.20
DENZO data reduction
PHENIX phasing
Coot model building