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_scbond_it 3.667
r_gen_planes_refined 0.011
r_scangle_it 5.262
r_angle_refined_deg 2.215
r_dihedral_angle_1_deg 6.443
r_mcbond_it 1.364
r_bond_refined_d 0.028
r_mcangle_it 2.177
r_dihedral_angle_3_deg 14.676
r_dihedral_angle_4_deg 19.76
r_chiral_restr 0.268
r_dihedral_angle_2_deg 34.426
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

Software
Software Name Purpose
XSCALE data scaling
MOLREP phasing
REFMAC refinement
PDB_EXTRACT data extraction version: 3.11
Macromolecular data collection version: crystallography data collector software