X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.5
Temperature 294.0
Details 5% PEG6000, pH 7.5, vapor diffusion, hanging drop, temperature 294K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 135.76 α = 90
b = 135.76 β = 90
c = 86.5 γ = 120
Symmetry
Space Group P 32 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 77
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315r -- 2011-04-16
Diffraction Radiation
Monochromator Protocol
Diamond (111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID14-4 1.28 ESRF ID14-4

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
3 50 99.5 -- -- -- -- 18753 18668 2.0 2.0 97.31

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 3.0 44.438 -- 1.99 18753 18666 934 99.62 -- 0.2643 0.2619 0.3096 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 3.0002 3.1584 -- 131 2478 0.3454 0.4006 -- 98.0
X Ray Diffraction 3.1584 3.3562 -- 132 2506 0.3265 0.3652 -- 100.0
X Ray Diffraction 3.3562 3.6152 -- 131 2506 0.3128 0.3691 -- 100.0
X Ray Diffraction 3.6152 3.9788 -- 133 2510 0.2866 0.3232 -- 100.0
X Ray Diffraction 3.9788 4.5541 -- 134 2548 0.2631 0.345 -- 100.0
X Ray Diffraction 4.5541 5.7357 -- 134 2546 0.2599 0.3129 -- 100.0
X Ray Diffraction 5.7357 44.4427 -- 139 2638 0.2236 0.2563 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 108.514
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 10.466
f_plane_restr 0.003
f_chiral_restr 0.033
f_angle_d 0.482
f_bond_d 0.002
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 5052
Nucleic Acid Atoms 0
Heterogen Atoms 34
Solvent Atoms 0

Software

Computing
Computing Package Purpose
ADSC Quantum Data Collection
XDS Data Reduction (intensity integration)
XDS Data Reduction (data scaling)
phaser Structure Solution
PHENIX (phenix.refine: 1.8.1_1168) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
phenix refinement