X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 5
Temperature 293.0
Details 100 mM citrate pH 5.0, 200 mM lithium chloride, 28% PEG 400, 5% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 113.92 α = 90
b = 143.1 β = 90
c = 178.37 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
PIXEL DECTRIS PILATUS 6M K-B Focusing Mirrors 2008-03-18
Diffraction Radiation
Monochromator Protocol
Liquid nitrogen-cooled double crystal, Si 111 SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL12-2 1.0 SSRL BL12-2

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
4.14 46.08 89.0 -- -- -- -- 22495 20129 -3.0 -3.0 --
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)
4.14 4.25 98.4 0.755 0.755 2.2 3.7 --

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 4.14 44.563 -- 0.0 22495 20129 1036 88.23 -- 0.2469 0.2441 0.3044 --
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 4.1401 4.3581 -- 123 2356 0.3218 0.4239 -- 78.0
X Ray Diffraction 4.3581 4.6309 -- 140 2507 0.2425 0.3148 -- 83.0
X Ray Diffraction 4.6309 4.9881 -- 134 2579 0.2018 0.2975 -- 84.0
X Ray Diffraction 4.9881 5.4892 -- 153 2675 0.2037 0.3241 -- 87.0
X Ray Diffraction 5.4892 6.2816 -- 155 2804 0.2379 0.3234 -- 91.0
X Ray Diffraction 6.2816 7.907 -- 169 3008 0.2454 0.3228 -- 97.0
X Ray Diffraction 7.907 44.5658 -- 162 3164 0.2495 0.2766 -- 97.0
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.016
f_chiral_restr 0.145
f_dihedral_angle_d 14.866
f_angle_d 2.766
f_bond_d 0.023
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 13797
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 0

Software

Computing
Computing Package Purpose
Bluice Data Collection
XDS Data Reduction (intensity integration)
SCALA Data Reduction (data scaling)
Phaser Structure Solution
PHENIX (phenix.refine: 1.8.1_1168) Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine: 1.8_1069) refinement
Phaser model building
Bluice data collection