X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.5
Temperature 277.0
Details 20% (w/v) PEGF-4000, 10% 2-propanol, 0.1 M HEPES, 50 mM 2-mercaptoethanol, 50 mM 2-hydroxyethyl disulfide

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 60.34 α = 90
b = 60.34 β = 90
c = 96.97 γ = 120
Symmetry
Space Group P 32 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315r -- 2009-07-23
Diffraction Radiation
Monochromator Protocol
two flat Si(111) crystals, mounted in a model DCM from Khozu SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ALS BEAMLINE 8.3.1 1.116 ALS 8.3.1

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
1.56 50 99.6 0.063 -- -- 8.1 -- 33182 -- -3.0 14.72
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)
1.56 1.66 99.2 0.494 -- 4.47 -- --

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 1.56 46.002 -- 1.99 -- 29630 1185 99.62 -- 0.1748 0.1736 0.2049 Random selection
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 1.56 1.631 -- 146 3499 0.2047 0.248 -- 99.0
X Ray Diffraction 1.631 1.717 -- 144 3479 0.1924 0.256 -- 100.0
X Ray Diffraction 1.717 1.8246 -- 146 3501 0.1815 0.2239 -- 100.0
X Ray Diffraction 1.8246 1.9655 -- 147 3541 0.1661 0.2182 -- 100.0
X Ray Diffraction 1.9655 2.1633 -- 148 3545 0.1597 0.1942 -- 100.0
X Ray Diffraction 2.1633 2.4763 -- 148 3550 0.1669 0.1829 -- 100.0
X Ray Diffraction 2.4763 3.1198 -- 150 3598 0.1842 0.2113 -- 100.0
X Ray Diffraction 3.1198 46.0217 -- 156 3732 0.1684 0.1947 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 17.1525
Anisotropic B[1][1] 0.243
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.243
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.486
RMS Deviations
Key Refinement Restraint Deviation
f_bond_d 0.013
f_dihedral_angle_d 13.198
f_angle_d 1.406
f_chiral_restr 0.078
f_plane_restr 0.007
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms --
Nucleic Acid Atoms --
Heterogen Atoms 22
Solvent Atoms 142

Software

Software
Software Name Purpose
XSCALE data scaling
PDB_EXTRACT data extraction version: 3.15
PHENIX refinement version: (phenix.refine: 1.7.1_743)
Coot model building