X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion
Temperature 295.0
Details 0.1 M HEPES 7.5, 0.1 M sodium chloride, and 1.6 M ammonium sulfate This solution with 20% glycerol was used as a cryoprotectant

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 133.49 α = 90
b = 134.87 β = 90
c = 39.56 γ = 90
Symmetry
Space Group C 2 2 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 210r -- 2016-08-10
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 19-BM 0.977 APS 19-BM

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
2.11 47.44 98.31 0.083 -- -- 6.3 -- 20254 -- -- 37.31
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)
2.11 2.15 99.2 0.639 -- -- 6.0 --

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 2.11 47.16 -- 0.0 -- 20254 1924 95.53 -- 0.2159 0.2138 0.2369 --
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 2.11 2.16 -- 125 1167 0.2593 0.2988 -- 88.74
X Ray Diffraction 2.16 2.22 -- 131 1213 0.2424 0.297 -- 88.95
X Ray Diffraction 2.22 2.28 -- 125 1244 0.2482 0.2976 -- 92.06
X Ray Diffraction 2.28 2.36 -- 131 1235 0.2195 0.2689 -- 92.67
X Ray Diffraction 2.36 2.44 -- 140 1266 0.2277 0.2901 -- 93.61
X Ray Diffraction 2.44 2.54 -- 132 1275 0.2196 0.2348 -- 94.68
X Ray Diffraction 2.54 2.65 -- 135 1304 0.2148 0.2562 -- 95.55
X Ray Diffraction 2.65 2.79 -- 140 1321 0.2128 0.2341 -- 96.63
X Ray Diffraction 2.79 2.97 -- 136 1334 0.2008 0.2293 -- 98.13
X Ray Diffraction 2.97 3.2 -- 144 1346 0.2037 0.222 -- 98.94
X Ray Diffraction 3.2 3.52 -- 139 1384 0.2051 0.229 -- 99.15
X Ray Diffraction 3.52 4.03 -- 144 1370 0.1968 0.2041 -- 99.41
X Ray Diffraction 4.03 5.08 -- 148 1400 0.1941 0.214 -- 99.29
X Ray Diffraction 5.08 47.16 -- 154 1471 0.2443 0.2593 -- 98.78
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 43.12
RMS Deviations
Key Refinement Restraint Deviation
f_angle_d 1.031
f_dihedral_angle_d 21.0048
f_bond_d 0.0062
f_chiral_restr 0.0571
f_plane_restr 0.0054
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1726
Nucleic Acid Atoms 0
Heterogen Atoms 6
Solvent Atoms 49

Software

Software
Software Name Purpose
HKL-2000 data reduction
HKL-2000 data scaling
PHASER phasing
PHENIX model building
PHENIX refinement
PDB_EXTRACT data extraction