X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
Temperature 294.15
Details Crystals were obtained at 21C in dark from a 1:1 mixture of protein (10-12 mg/mL) and a reservoir solution consisting of 7.5% PEG 6000 and 0.1 M HEPES pH 7.1. Crystal reached maximum size after 4-5 days and were harvested at that time in the dark. Crystals were transferred to cryoprotectant solution consisting of 5% PEG 6000, 0.1 M HEPES pH 7, 2 mM DTT and either 30% P400 or 30% glycerol. Crystals were flash-frozen in liquid nitrogen in the dark

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 53.73 α = 90
b = 85.57 β = 90
c = 103.28 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 -- 2018-09-14
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ALS BEAMLINE 8.2.1 1.0000 ALS 8.2.1

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
1.79 50 85.3 0.077 -- -- 4.0 -- 38744 -- -- --
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)
1.793 1.86 -- 0.389 -- -- -- --

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 1.793 44.214 -- 1.35 -- 38708 2000 85.2 -- 0.1652 0.1629 0.2061 --
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 1.793 1.8375 -- 128 2350 0.1848 0.2212 0.0 78.0
X Ray Diffraction 1.8375 1.8872 -- 141 2575 0.1816 0.2578 0.0 85.0
X Ray Diffraction 1.8872 1.9427 -- 147 2724 0.1784 0.249 0.0 89.0
X Ray Diffraction 1.9427 2.0054 -- 149 2717 0.1757 0.2158 0.0 90.0
X Ray Diffraction 2.0054 2.0771 -- 147 2703 0.1719 0.2397 0.0 89.0
X Ray Diffraction 2.0771 2.1603 -- 148 2713 0.1636 0.2058 0.0 89.0
X Ray Diffraction 2.1603 2.2586 -- 146 2684 0.161 0.2003 0.0 88.0
X Ray Diffraction 2.2586 2.3777 -- 145 2667 0.1584 0.2033 0.0 88.0
X Ray Diffraction 2.3777 2.5266 -- 147 2689 0.1502 0.1809 0.0 87.0
X Ray Diffraction 2.5266 2.7217 -- 143 2624 0.1533 0.1993 0.0 86.0
X Ray Diffraction 2.7217 2.9955 -- 142 2611 0.1628 0.2122 0.0 84.0
X Ray Diffraction 2.9955 3.4288 -- 140 2571 0.1563 0.2157 0.0 83.0
X Ray Diffraction 3.4288 4.3194 -- 138 2540 0.1458 0.1963 0.0 81.0
X Ray Diffraction 4.3194 44.214 -- 139 2540 0.1809 0.1865 0.0 77.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 24.5508
RMS Deviations
Key Refinement Restraint Deviation
f_chiral_restr 0.054
f_plane_restr 0.006
f_dihedral_angle_d 16.364
f_angle_d 0.895
f_bond_d 0.007
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3930
Nucleic Acid Atoms 0
Heterogen Atoms 109
Solvent Atoms 404

Software

Software
Software Name Purpose
PHENIX refinement version: 1.12_2829
PDB_EXTRACT data extraction version: 3.25
HKL-2000 data reduction
HKL-2000 data scaling
PHENIX phasing