X-RAY DIFFRACTION Experimental Data & Validation


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Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 6
Temperature 298.0
Details 15% isopropanol, 0.1 M potassium chloride, 25 mM magnesium chloride, 2% 1,4-dioxane, 50 mM sodium cacodylate, pH 6.0, cryoprotectant: Paratone N, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 66.38 α = 90
b = 129.57 β = 90
c = 54.3 γ = 90
Symmetry
Space Group C 2 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD RIGAKU Varimax optics 2010-05
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU FR-E+ SUPERBRIGHT 1.5418 -- --

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
2.2 64.79 99.9 -- 0.043 -- 7.0 12258 12258 -- -- --
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)
2.2 2.32 100.0 0.214 0.214 3.5 7.0 1754

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 2.2 24.67 -- 0.0 -- 12255 585 99.85 -- 0.2328 0.2302 0.2828 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 2.2 2.257 -- 42 840 0.332 0.406 -- 99.89
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 33.9067
Anisotropic B[1][1] 0.82
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -1.53
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.71
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 3.377
r_scbond_it 2.282
r_mcangle_it 1.573
r_mcbond_other 0.166
r_bond_refined_d 0.018
r_bond_other_d 0.001
r_angle_refined_deg 1.609
r_angle_other_deg 0.978
r_dihedral_angle_1_deg 6.821
r_dihedral_angle_2_deg 34.694
r_dihedral_angle_3_deg 16.82
r_dihedral_angle_4_deg 15.977
r_chiral_restr 0.094
r_gen_planes_refined 0.007
r_gen_planes_other 0.001
r_mcbond_it 0.855
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1751
Nucleic Acid Atoms 0
Heterogen Atoms 8
Solvent Atoms 69

Software

Computing
Computing Package Purpose
XDS Data Reduction (intensity integration)
SCALA Data Reduction (data scaling)
Molrep Structure Solution
REFMAC 5.5.0102 Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.10 data extraction
REFMAC5 version: 5.5.0102 refinement
SCALA version: 3.3.15 data reduction