X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.5
Temperature 291.0
Details 25% PEG 3350, 0.1 M Ammonium Sulfate, 0.1 M BisTris pH6.5, vapor diffusion hanging drop, temperature 291K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 118.05 α = 90
b = 134.48 β = 90
c = 137.26 γ = 90
Symmetry
Space Group C 2 2 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD Marmosaic CCD300 -- 2012-01-25
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON CLSI BEAMLINE 08ID-1 0.97949 CLSI 08ID-1

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
1.7 50 99.7 0.089 0.089 -- 7.4 -- 119046 -- -- 21.8
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)
1.7 1.73 99.4 0.635 -- -- 7.0 5879

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 1.7 50.0 -- 0.0 -- 118841 1202 99.45 -- 0.1988 0.1986 0.2226 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 1.7 1.744 -- 93 8528 0.234 0.233 -- 98.22
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 24.8969
Anisotropic B[1][1] -0.11
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.64
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.53
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 2.657
r_scbond_it 1.598
r_mcangle_it 1.128
r_mcbond_it 0.591
r_gen_planes_refined 0.004
r_chiral_restr 0.072
r_dihedral_angle_4_deg 9.708
r_dihedral_angle_3_deg 11.947
r_dihedral_angle_2_deg 34.422
r_dihedral_angle_1_deg 5.551
r_angle_refined_deg 1.108
r_bond_refined_d 0.008
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 7552
Nucleic Acid Atoms 0
Heterogen Atoms 273
Solvent Atoms 953

Software

Computing
Computing Package Purpose
HKL-3000 Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
MOLREP Structure Solution
REFMAC 5.5.0109, COOT 0.6 Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
REFMAC5 refinement
SCALEPACK data reduction