X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8
Temperature 293.0
Details 0.1M TRIS pH 8.0, 1% PEG400, 1.9M (NH4)2SO4, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 103.02 α = 90
b = 107.26 β = 90
c = 142.21 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC Quantum Q315r -- 2012-04-17
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRF BEAMLINE BL17U 0.979 SSRF BL17U

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
2.22 48.43 99.1 0.18 -- -- -- -- 77829 -- -3.0 50.167
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)
2.22 2.35 94.8 0.016 -- 1.05 -- --

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 2.7199 48.431 -- 2.01 -- 43017 1291 99.96 -- 0.2068 0.2047 0.2748 --
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 2.7199 2.8288 -- 142 4585 0.2543 0.3387 -- 100.0
X Ray Diffraction 2.8288 2.9576 -- 141 4551 0.2558 0.37 -- 100.0
X Ray Diffraction 2.9576 3.1135 -- 142 4591 0.2417 0.3539 -- 100.0
X Ray Diffraction 3.1135 3.3085 -- 142 4591 0.2142 0.2921 -- 100.0
X Ray Diffraction 3.3085 3.5639 -- 142 4594 0.2013 0.2904 -- 100.0
X Ray Diffraction 3.5639 3.9224 -- 142 4603 0.1882 0.2621 -- 100.0
X Ray Diffraction 3.9224 4.4896 -- 144 4653 0.1787 0.2643 -- 100.0
X Ray Diffraction 4.4896 5.655 -- 145 4693 0.184 0.226 -- 100.0
X Ray Diffraction 5.655 48.4385 -- 151 4865 0.2129 0.2445 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 24.843
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.005
f_chiral_restr 0.093
f_dihedral_angle_d 18.66
f_angle_d 1.376
f_bond_d 0.01
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 10574
Nucleic Acid Atoms 0
Heterogen Atoms 155
Solvent Atoms 24

Software

Computing
Computing Package Purpose
Bluice Data Collection
XDS Data Reduction (intensity integration)
XSCALE Data Reduction (data scaling)
PHASER Structure Solution
PHENIX (phenix.refine: 1.8_1069) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
phenix refinement
Phaser version: 2.3.0 molecular replacement
Xscale data reduction