X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8.5
Temperature 289.0
Details PEG 4000, 0.2M LiSO4, 0.1M Tris-HCl

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 98.4 α = 90
b = 98.4 β = 90
c = 80.18 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 RIGAKU SATURN 944 -- 2008-12-24
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU MICROMAX-007 1.54 -- --

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
2.5 50 99.9 0.134 -- 19.537 10.7 -- 15344 -- -- --
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)
2.5 2.59 99.9 0.931 -- -- 9.8 1536

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 2.502 32.208 -- 1.34 -- 15297 765 99.83 -- 0.1818 0.1802 0.2129 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 2.502 2.6951 -- 147 2884 0.2449 0.2861 -- 100.0
X Ray Diffraction 2.6951 2.9662 -- 167 2871 0.2416 0.2511 -- 100.0
X Ray Diffraction 2.9662 3.395 -- 149 2916 0.2013 0.227 -- 100.0
X Ray Diffraction 3.395 4.2757 -- 160 2902 0.165 0.199 -- 100.0
X Ray Diffraction 4.2757 32.2103 -- 142 2959 0.1474 0.1851 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 47.0485
RMS Deviations
Key Refinement Restraint Deviation
f_bond_d 0.003
f_plane_restr 0.003
f_dihedral_angle_d 14.238
f_angle_d 0.634
f_chiral_restr 0.028
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2218
Nucleic Acid Atoms 0
Heterogen Atoms 40
Solvent Atoms 87

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
PHASER phasing
PHENIX refinement version: (phenix.refine: 1.9_1692)
PDB_EXTRACT data extraction version: 3.15
Blu-Ice data collection