X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.5
Temperature 293.0
Details 1.6M-1.7M Ammonium sulphate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 69.78 α = 90
b = 61.64 β = 112.08
c = 71.37 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 300 mm CCD DCM with cryo-cooled 1st crystal sagittally bent 2nd crystal followed by vertically focusing 2011-01-26
Diffraction Radiation
Monochromator Protocol
20mm hydrid small gap in-vacuum undulator SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON CLSI BEAMLINE 08ID-1 0.979490 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
1.54 50 85.0 0.046 -- -- -- -- 70712 -- -3.0 31.727
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)
1.54 1.58 32.7 0.015 -- 0.44 -- --

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 1.8 66.08 -- 0.0 -- 50390 2633 99.02 -- 0.1952 0.19 0.223 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 1.8 1.847 -- 178 3283 0.274 0.311 -- 90.06
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 29.1315
Anisotropic B[1][1] 1.44
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 1.81
Anisotropic B[2][2] -1.68
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 1.59
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 5.262
r_scbond_it 3.667
r_mcangle_it 2.177
r_mcbond_it 1.364
r_gen_planes_refined 0.011
r_chiral_restr 0.268
r_dihedral_angle_4_deg 19.76
r_dihedral_angle_3_deg 14.676
r_dihedral_angle_2_deg 34.426
r_dihedral_angle_1_deg 6.443
r_angle_refined_deg 2.215
r_bond_refined_d 0.028
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3916
Nucleic Acid Atoms 0
Heterogen Atoms 52
Solvent Atoms 116

Software

Computing
Computing Package Purpose
Macromolecular crystallography data collector software Data Collection
XSCALE Data Reduction (intensity integration)
XSCALE Data Reduction (data scaling)
MOLREP Structure Solution
REFMAC 5.5.0110 Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
REFMAC5 refinement
MOLREP molecular replacement
Xscale data reduction