X-RAY DIFFRACTION Experimental Data & Validation


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Crystallization

Crystalization Experiments
Details 0.1 M SUCCINATE PHOSPHATE GLYCINE BUFFER PH 6, 30% PEG1K, 0.5% DMSO, SITTING DROP

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 98.89 α = 90
b = 98.89 β = 90
c = 81.03 γ = 120
Symmetry
Space Group P 65

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARRESEARCH MIRRORS 2005-04-23
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SLS BEAMLINE X10SA -- 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
2.05 50 96.7 0.1 -- -- 3.3 -- 27388 -- 2.0 --
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)
2.05 2.15 80.0 0.44 -- 2.0 2.0 --

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 2.05 85.75 -- -- -- 25947 1381 96.7 -- 0.185 0.183 0.221 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 2.05 2.1 -- 63 1444 0.328 0.452 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 34.77
Anisotropic B[1][1] 0.61
Anisotropic B[1][2] 0.31
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.61
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.92
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 2.615
r_scbond_it 1.626
r_mcangle_it 1.364
r_mcbond_it 0.919
r_nbd_refined 0.184
r_gen_planes_other 0.001
r_gen_planes_refined 0.005
r_chiral_restr 0.074
r_dihedral_angle_4_deg 14.499
r_dihedral_angle_3_deg 13.717
r_dihedral_angle_2_deg 33.78
r_dihedral_angle_1_deg 5.475
r_angle_other_deg 0.846
r_angle_refined_deg 1.39
r_bond_other_d 0.001
r_bond_refined_d 0.013
r_nbd_other 0.18
r_nbtor_refined 0.176
r_nbtor_other 0.081
r_xyhbond_nbd_refined 0.154
r_symmetry_vdw_refined 0.053
r_symmetry_vdw_other 0.314
r_symmetry_hbond_refined 0.132
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2213
Nucleic Acid Atoms 0
Heterogen Atoms 36
Solvent Atoms 140

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
PHASER Structure Solution
REFMAC 5.2.0005 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.2.0005 refinement
PHASER model building