X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.1
Temperature 277.15
Details 2.2 M sodium/potassium phosphate, pH 7.1, 50 mM 2-mercaptoethanol, 50 mM 2-hydroxyethyl disulfide

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 60.16 α = 90
b = 60.16 β = 90
c = 96.81 γ = 120
Symmetry
Space Group P 32 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315r -- 2015-06-07
Diffraction Radiation
Monochromator Protocol
KHOZU Double flat crystal SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ALS BEAMLINE 8.3.1 0.95372 ALS 8.3.1

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
1.3 45.88 99.9 0.07 -- -- 8.0 -- 50446 -- -- --
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)
1.3 1.35 100.0 0.327 -- -- -- --

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 1.3 45.878 -- 1.36 -- 50443 2568 99.8 -- 0.1848 0.1838 0.2035 --
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 1.3001 1.3251 -- 152 2629 0.2621 0.3215 -- 100.0
X Ray Diffraction 1.3251 1.3521 -- 154 2603 0.2476 0.237 -- 100.0
X Ray Diffraction 1.3521 1.3815 -- 151 2617 0.2211 0.2397 -- 100.0
X Ray Diffraction 1.3815 1.4137 -- 136 2605 0.2237 0.2499 -- 100.0
X Ray Diffraction 1.4137 1.449 -- 130 2669 0.2072 0.2469 -- 100.0
X Ray Diffraction 1.449 1.4882 -- 157 2612 0.1966 0.2127 -- 100.0
X Ray Diffraction 1.4882 1.532 -- 143 2639 0.189 0.1908 -- 100.0
X Ray Diffraction 1.532 1.5814 -- 135 2661 0.1915 0.2304 -- 100.0
X Ray Diffraction 1.5814 1.638 -- 134 2622 0.1863 0.1984 -- 100.0
X Ray Diffraction 1.638 1.7035 -- 140 2644 0.1808 0.2245 -- 100.0
X Ray Diffraction 1.7035 1.7811 -- 155 2645 0.1809 0.2072 -- 100.0
X Ray Diffraction 1.7811 1.875 -- 158 2644 0.1897 0.2389 -- 100.0
X Ray Diffraction 1.875 1.9925 -- 123 2662 0.1851 0.198 -- 100.0
X Ray Diffraction 1.9925 2.1463 -- 143 2691 0.1719 0.2025 -- 100.0
X Ray Diffraction 2.1463 2.3623 -- 144 2670 0.174 0.1812 -- 100.0
X Ray Diffraction 2.3623 2.7041 -- 120 2737 0.178 0.2081 -- 100.0
X Ray Diffraction 2.7041 3.4067 -- 138 2719 0.1758 0.1941 -- 100.0
X Ray Diffraction 3.4067 45.9068 -- 155 2806 0.1711 0.1729 -- 98.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 14.8316
RMS Deviations
Key Refinement Restraint Deviation
f_bond_d 0.006
f_chiral_restr 0.068
f_dihedral_angle_d 12.164
f_angle_d 0.824
f_plane_restr 0.005
Coordinate Error
Parameter Value
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1283
Nucleic Acid Atoms 0
Heterogen Atoms 16
Solvent Atoms 367

Software

Software
Software Name Purpose
PHENIX refinement version: 1.10.1_2155
PDB_EXTRACT data extraction version: 3.20
d*TREK data reduction version: 9.9.9.10L
PHENIX model building
PHENIX phasing
d*TREK data scaling version: 9.9.9.10L