X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 6
Temperature 295.0
Details 0.1 M MES monohydrate pH 6.0, 2.4 M ammonium sulfate

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 34.33 α = 90
b = 40.61 β = 90
c = 101.91 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
IMAGE PLATE RIGAKU RAXIS HTC -- 2015-10-20
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU MICROMAX-007 HF 1.54178 -- --

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
1.41 40.61 90.2 -- 0.041 -- 6.4 -- 25403 -- -- 10.5
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)
1.41 1.49 77.9 0.111 -- 13.0 6.6 --

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 1.411 28.471 -- 1.4 -- 25341 1999 89.78 -- 0.1575 0.1543 0.1954 --
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 1.4114 1.4467 -- 107 1249 0.1324 0.2051 -- 68.0
X Ray Diffraction 1.4467 1.4858 -- 134 1564 0.1287 0.1988 -- 87.0
X Ray Diffraction 1.4858 1.5295 -- 135 1579 0.1269 0.2084 -- 87.0
X Ray Diffraction 1.5295 1.5789 -- 138 1609 0.1232 0.2085 -- 88.0
X Ray Diffraction 1.5789 1.6353 -- 139 1627 0.1324 0.1855 -- 88.0
X Ray Diffraction 1.6353 1.7008 -- 141 1640 0.1376 0.1985 -- 90.0
X Ray Diffraction 1.7008 1.7782 -- 142 1652 0.1442 0.1904 -- 90.0
X Ray Diffraction 1.7782 1.8719 -- 145 1693 0.1478 0.2004 -- 92.0
X Ray Diffraction 1.8719 1.9892 -- 145 1693 0.1413 0.2045 -- 92.0
X Ray Diffraction 1.9892 2.1427 -- 148 1739 0.1446 0.1727 -- 93.0
X Ray Diffraction 2.1427 2.3582 -- 149 1742 0.1479 0.2007 -- 95.0
X Ray Diffraction 2.3582 2.6992 -- 154 1791 0.1576 0.204 -- 95.0
X Ray Diffraction 2.6992 3.3999 -- 156 1828 0.1673 0.175 -- 96.0
X Ray Diffraction 3.3999 28.477 -- 166 1936 0.181 0.2072 -- 96.0
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.006
f_bond_d 0.007
f_angle_d 0.899
f_chiral_restr 0.081
f_dihedral_angle_d 15.131
Coordinate Error
Parameter Value
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1169
Nucleic Acid Atoms 0
Heterogen Atoms 16
Solvent Atoms 220

Software

Software
Software Name Purpose
PHENIX refinement version: (1.10_2155)
XDS data reduction
XDS data scaling
PHENIX phasing