X-RAY DIFFRACTION Experimental Data & Validation


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Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.2
Temperature 289.0
Details 0.15 M sodium formate, 20% PEG 3350, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 289K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 68.14 α = 90
b = 97.71 β = 97.32
c = 70.67 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 225 mm CCD beryllium lens 2012-11-10
Diffraction Radiation
Monochromator Protocol
C(111) diamond laue monochromator SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 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
1.85 50 99.9 0.082 -- -- 3.8 78447 78447 0.0 -3.0 --
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)
1.85 1.88 100.0 0.683 -- -- 3.8 --

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 1.85 40.11 -- 0.0 74288 74288 3936 99.86 0.14971 0.14971 0.14845 0.17304 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 1.85 1.898 -- 274 5494 0.216 0.259 -- 99.98
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 30.652
Anisotropic B[1][1] 1.41
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 1.02
Anisotropic B[2][2] -1.29
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.24
RMS Deviations
Key Refinement Restraint Deviation
r_gen_planes_other 0.006
r_gen_planes_refined 0.01
r_chiral_restr 0.111
r_dihedral_angle_4_deg 17.153
r_dihedral_angle_3_deg 11.033
r_dihedral_angle_2_deg 36.904
r_dihedral_angle_1_deg 5.981
r_angle_other_deg 1.522
r_angle_refined_deg 1.88
r_bond_other_d 0.009
r_bond_refined_d 0.018
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 7048
Nucleic Acid Atoms 0
Heterogen Atoms 232
Solvent Atoms 568

Software

Computing
Computing Package Purpose
LS-CAT modified MD-2 Data Collection
HKL-3000 Data Reduction (intensity integration)
HKL-3000 Data Reduction (data scaling)
HKL-3000,MOLREP Structure Solution
REFMAC 5.7.0029 Structure Refinement
Software
Software Name Purpose
HKL-3000 refinement
COOT refinement
REFMAC version: 5.7.0029 refinement
MOLREP model building
HKL-3000 model building
LS-CAT version: modified MD-2 data collection