X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 8.5
Temperature 277.0
Details 100 mM TRIS pH 8.5 12.5 % PEG 3350 (v/v)

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 64.52 α = 90
b = 87.26 β = 94.01
c = 66.15 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD RAYONIX MX-300 mirrors 2015-06-04
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON CLSI BEAMLINE 08B1-1 0.979 CLSI 08B1-1

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
2.25 39.67 98.3 -- -- -- 2.8 -- 36580 -- -- --
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)
2.2 2.6 97.4 -- -- -- 2.8 --

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 2.4 39.674 -- 1.36 -- 28179 1534 98.16 -- 0.2083 0.2071 0.2285 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 2.4 2.4775 -- 147 2441 0.2925 0.3347 -- 99.0
X Ray Diffraction 2.4775 2.566 -- 144 2404 0.2841 0.2934 -- 99.0
X Ray Diffraction 2.566 2.6687 -- 140 2426 0.267 0.3147 -- 99.0
X Ray Diffraction 2.6687 2.7902 -- 140 2438 0.2603 0.2612 -- 99.0
X Ray Diffraction 2.7902 2.9372 -- 130 2433 0.2458 0.2667 -- 99.0
X Ray Diffraction 2.9372 3.1212 -- 153 2424 0.225 0.2693 -- 99.0
X Ray Diffraction 3.1212 3.362 -- 128 2424 0.2169 0.2504 -- 98.0
X Ray Diffraction 3.362 3.7002 -- 148 2407 0.203 0.2054 -- 97.0
X Ray Diffraction 3.7002 4.2351 -- 131 2405 0.1789 0.2001 -- 98.0
X Ray Diffraction 4.2351 5.3337 -- 127 2437 0.1579 0.1821 -- 97.0
X Ray Diffraction 5.3337 39.679 -- 146 2406 0.1876 0.1954 -- 95.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 51.5
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.002
f_angle_d 0.733
f_chiral_restr 0.03
f_dihedral_angle_d 15.043
f_bond_d 0.003
Coordinate Error
Parameter Value
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4034
Nucleic Acid Atoms 0
Heterogen Atoms 66
Solvent Atoms 178

Software

Software
Software Name Purpose
PHENIX refinement version: 1.9_1692
XDS data reduction
XDS data scaling
PHASER phasing