X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8.5
Temperature 277.0
Details 30% PEG 4000, 0.1M Tris, and 0.2 M MgCl2 , pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 66.32 α = 90
b = 163.48 β = 90
c = 36.74 γ = 90
Symmetry
Space Group P 21 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD RIGAKU SATURN 92 -- 2010-09-25
Diffraction Radiation
Monochromator Protocol
Mirrors SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5418 -- --

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
2.31 35 96.0 0.05 -- -- -- 17621 17621 1.0 -3.0 39.42
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)
2.31 2.37 83.2 0.244 -- 6.4 -- --

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 2.31 33.511 -- 1.99 17611 17611 880 95.92 -- 0.1998 0.1973 0.2465 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 2.3071 2.4516 -- 136 2621 0.2447 0.3008 -- 92.0
X Ray Diffraction 2.4516 2.6408 -- 150 2849 0.2218 0.3141 -- 100.0
X Ray Diffraction 2.6408 2.9065 -- 150 2848 0.2177 0.2639 -- 100.0
X Ray Diffraction 2.9065 3.3267 -- 153 2896 0.2032 0.2426 -- 100.0
X Ray Diffraction 3.3267 4.19 -- 129 2453 0.2096 0.2627 -- 84.0
X Ray Diffraction 4.19 33.5141 -- 162 3064 0.1612 0.2002 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 35.917
Anisotropic B[1][1] 12.9745
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -10.1732
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -2.8013
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 12.272
f_plane_restr 0.003
f_chiral_restr 0.053
f_angle_d 0.721
f_bond_d 0.004
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2830
Nucleic Acid Atoms 0
Heterogen Atoms 9
Solvent Atoms 208

Software

Computing
Computing Package Purpose
StructureStudio Data Collection
XDS Data Reduction (intensity integration)
XSCALE Data Reduction (data scaling)
PHASER Structure Solution
PHENIX (phenix.refine: 1.6.4_486) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.10 data extraction
phenix refinement
Xscale data processing