X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7
Temperature 298.0
Details HEPES pH 7.0, ammonium sulfate, DMSO, PEG 8000, L-glutathione reduced/oxidized, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 32.09 α = 108.5
b = 36.51 β = 90.29
c = 43.75 γ = 111.13
Symmetry
Space Group P 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 210r -- 2009-02-18
Diffraction Radiation
Monochromator Protocol
Sagitally focused Si SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX1 0.9537 AUSTRALIAN SYNCHROTRON MX1

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
1.58 41.11 96.4 0.05 -- -- 3.9 23811 22922 0.0 0.0 17.7
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)
1.58 1.64 91.8 0.35 -- 3.26 3.6 2182

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 1.581 29.657 -- 0.15 22923 22042 1133 92.54 -- 0.1647 0.1629 0.1969 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 1.5807 1.6527 -- 119 2254 0.2105 0.264 -- 80.0
X Ray Diffraction 1.6527 1.7398 -- 125 2480 0.2071 0.2659 -- 87.0
X Ray Diffraction 1.7398 1.8488 -- 148 2565 0.1915 0.2693 -- 91.0
X Ray Diffraction 1.8488 1.9915 -- 150 2629 0.1723 0.2101 -- 94.0
X Ray Diffraction 1.9915 2.1918 -- 145 2717 0.15 0.1997 -- 96.0
X Ray Diffraction 2.1918 2.5089 -- 137 2730 0.1489 0.1947 -- 97.0
X Ray Diffraction 2.5089 3.1603 -- 152 2779 0.1549 0.1871 -- 98.0
X Ray Diffraction 3.1603 29.6618 -- 157 2755 0.1607 0.1766 -- 98.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 24.982
Anisotropic B[1][1] -4.4699
Anisotropic B[1][2] 4.1221
Anisotropic B[1][3] 2.0215
Anisotropic B[2][2] 6.2901
Anisotropic B[2][3] 0.6596
Anisotropic B[3][3] -1.8202
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 19.733
f_plane_restr 0.009
f_chiral_restr 0.086
f_angle_d 1.431
f_bond_d 0.014
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.18
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1624
Nucleic Acid Atoms 0
Heterogen Atoms 15
Solvent Atoms 153

Software

Computing
Computing Package Purpose
Blu-Ice GUI Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
PHASER Structure Solution
PHENIX (phenix.refine: 1.7_650) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.10 data extraction
phenix refinement
Phaser version: 2.1.4 molecular replacement
HKL data reduction