X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7.5
Temperature 298.0
Details 150mM D-glucose, 100mM HEPES/MOPS pH7.5, 40% Glycerol/PEG4000

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 68.16 α = 90
b = 78.24 β = 90
c = 203.86 γ = 90
Symmetry
Space Group P 2 2 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD RAYONIX MX-300 -- 2014-05-22
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON NSRRC BEAMLINE BL13B1 1.0 NSRRC BL13B1

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
3.5 20 94.7 0.196 -- 3.979 2.9 -- 13561 -- -- 58.37
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)
3.5 3.62 97.1 0.478 -- -- 2.8 1362

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 3.5 19.727 -- 1.33 -- 13555 683 94.78 -- 0.2339 0.2313 0.282 --
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 3.5002 3.7688 -- 140 2577 0.2944 0.3513 -- 97.0
X Ray Diffraction 3.7688 4.1449 -- 145 2564 0.2552 0.3147 -- 96.0
X Ray Diffraction 4.1449 4.7374 -- 129 2570 0.2114 0.2657 -- 96.0
X Ray Diffraction 4.7374 5.9414 -- 119 2578 0.2134 0.2765 -- 94.0
X Ray Diffraction 5.9414 19.7277 -- 150 2583 0.2089 0.2369 -- 91.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 55.274
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.005
f_bond_d 0.005
f_angle_d 1.019
f_dihedral_angle_d 15.3
f_chiral_restr 0.041
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4972
Nucleic Acid Atoms 0
Heterogen Atoms 26
Solvent Atoms 0

Software

Software
Software Name Purpose
PHENIX refinement version: dev_1819
SCALA data reduction
HKL-2000 data scaling
PHASER phasing