X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8
Temperature 298.0
Details 0.1 M Tris (pH 8.0), 0.2 M Li2SO4, 30% (w/v) PEG 3350

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 43.04 α = 90
b = 58.27 β = 90
c = 111.1 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 -- 2013-07-20
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON NSRRC BEAMLINE BL13C1 0.97622 NSRRC BL13C1

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
2.23 30 98.6 0.081 -- 22.924 6.1 -- 14016 -- -- --
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)
2.23 2.31 89.8 0.273 -- -- 4.5 1249

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 2.23 25.801 -- 0.0 -- 12764 1269 89.8 -- 0.2084 0.204 0.2486 --
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 2.23 2.3192 -- 89 820 0.2416 0.332 -- 59.0
X Ray Diffraction 2.3192 2.4247 -- 106 990 0.2617 0.2901 -- 70.0
X Ray Diffraction 2.4247 2.5524 -- 128 1172 0.2611 0.3526 -- 85.0
X Ray Diffraction 2.5524 2.7122 -- 153 1364 0.2467 0.2977 -- 97.0
X Ray Diffraction 2.7122 2.9213 -- 151 1377 0.2431 0.2827 -- 98.0
X Ray Diffraction 2.9213 3.2148 -- 154 1392 0.2293 0.2801 -- 99.0
X Ray Diffraction 3.2148 3.6788 -- 159 1418 0.1851 0.2216 -- 99.0
X Ray Diffraction 3.6788 4.6306 -- 160 1441 0.1622 0.1924 -- 100.0
X Ray Diffraction 4.6306 25.8026 -- 169 1521 0.1758 0.2219 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 29.76
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.004
f_bond_d 0.003
f_angle_d 0.725
f_dihedral_angle_d 19.762
f_chiral_restr 0.031
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2042
Nucleic Acid Atoms 0
Heterogen Atoms 56
Solvent Atoms 81

Software

Software
Software Name Purpose
Blu-Ice data collection
HKL-2000 data scaling
PHASER phasing version: 2.5.3
PHENIX refinement version: 1.8.4_1496
PDB_EXTRACT data extraction version: 3.15