X-RAY DIFFRACTION Experimental Data & Validation


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Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.2
Temperature 293.0
Details 100mM MES, 25% PEG 4000, 50mM n-BOG, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 64 α = 90
b = 68.8 β = 90
c = 74.8 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 90
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD PSI PILATUS 6M Dynamic bendable mirror 2011-03-20
Diffraction Radiation
Monochromator Protocol
Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SLS BEAMLINE X10SA 0.978600 SLS X10SA

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
2.4 48.63 99.8 0.075 -- -- 5.18 13430 13405 -- -3.0 45.312
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)
2.4 2.5 99.6 0.438 -- 3.95 -- --

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 2.4 48.63 -- 0.0 13430 13405 805 99.8 0.216 0.2197 0.2147 0.2974 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 2.4 2.462 -- 59 915 0.259 0.341 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 37.1833
Anisotropic B[1][1] -0.75
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 1.7
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.95
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 2.854
r_scbond_it 1.991
r_mcangle_it 1.38
r_mcbond_it 1.014
r_symmetry_hbond_refined 0.21
r_bond_refined_d 0.014
r_angle_refined_deg 1.488
r_dihedral_angle_1_deg 6.528
r_dihedral_angle_2_deg 36.845
r_dihedral_angle_3_deg 20.241
r_dihedral_angle_4_deg 21.991
r_chiral_restr 0.096
r_gen_planes_refined 0.005
r_nbd_refined 0.221
r_nbtor_refined 0.306
r_xyhbond_nbd_refined 0.161
r_symmetry_vdw_refined 0.202
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2680
Nucleic Acid Atoms 0
Heterogen Atoms 69
Solvent Atoms 50

Software

Computing
Computing Package Purpose
XDS Data Collection
XSCALE Data Reduction (intensity integration)
XSCALE Data Reduction (data scaling)
PHASER Structure Solution
REFMAC 5.2.0005 Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.10 data extraction
REFMAC5 refinement
Phaser molecular replacement
Xscale data reduction