X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 6.5
Temperature 289.0
Details 0.085 M MES pH 6.5, 25.5 % (w/v) PEG 5000 monomethyl ether, 15 %(v/v) Glycerol

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 63.67 α = 90
b = 77.31 β = 90
c = 149.66 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 315r -- 2014-11-17
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRF BEAMLINE BL17U 0.97892 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
2.5 60 99.6 0.06 -- 20.14 4.3 -- 26095 -- -- 54.03
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 2.59 100.0 0.482 -- -- 4.3 2541

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 2.503 32.265 -- 1.34 -- 26045 1328 99.48 -- 0.2017 0.1994 0.2439 --
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 2.5031 2.6032 -- 151 2631 0.2656 0.3537 -- 98.0
X Ray Diffraction 2.6032 2.7217 -- 135 2734 0.2566 0.3089 -- 100.0
X Ray Diffraction 2.7217 2.8651 -- 154 2726 0.2481 0.3121 -- 100.0
X Ray Diffraction 2.8651 3.0445 -- 144 2714 0.2338 0.3067 -- 100.0
X Ray Diffraction 3.0445 3.2793 -- 146 2713 0.217 0.2928 -- 100.0
X Ray Diffraction 3.2793 3.6089 -- 141 2747 0.1998 0.2409 -- 100.0
X Ray Diffraction 3.6089 4.1302 -- 147 2757 0.1776 0.2055 -- 99.0
X Ray Diffraction 4.1302 5.2001 -- 149 2793 0.1739 0.2277 -- 100.0
X Ray Diffraction 5.2001 32.2677 -- 161 2902 0.1921 0.2158 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 59.054
RMS Deviations
Key Refinement Restraint Deviation
f_bond_d 0.008
f_chiral_restr 0.047
f_angle_d 1.198
f_dihedral_angle_d 16.083
f_plane_restr 0.006
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3681
Nucleic Acid Atoms 471
Heterogen Atoms 43
Solvent Atoms 144

Software

Software
Software Name Purpose
PHENIX refinement version: phenix.refine: 1.9_1692
HKL-2000 data scaling
PDB_EXTRACT data extraction version: 3.15
HKL-2000 data reduction
PHASER phasing