X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Evaporation
pH 7.5
Temperature 277.0
Details 0.1 M HEPES sodium, pH 7.5, 1M Sodium citrate tribasic dihydrate, and 10 mM TCEP

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 51.43 α = 90
b = 51.43 β = 90
c = 336.57 γ = 120
Symmetry
Space Group P 61 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD RAYONIX MX-225 K-B mirrors 2017-11-07
Diffraction Radiation
Monochromator Protocol
liquid nitrogen cooled double crystal SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SPRING-8 BEAMLINE BL32XU 1 SPring-8 BL32XU

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
2.1 41.4 98.4 0.0198 -- -- 1.99963 -- 16418 -- -- 40.85
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)
2.1 2.175 97.4 0.3512 -- -- 2.0 --

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 2.1 41.397 -- 1.34 -- 16399 820 98.42 -- 0.1963 0.1937 0.2468 --
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 2.1001 2.2316 -- 131 2518 0.2493 0.2972 -- 98.0
X Ray Diffraction 2.2316 2.4039 -- 130 2463 0.2245 0.3066 -- 98.0
X Ray Diffraction 2.4039 2.6458 -- 133 2523 0.2223 0.2566 -- 98.0
X Ray Diffraction 2.6458 3.0286 -- 136 2578 0.2067 0.235 -- 98.0
X Ray Diffraction 3.0286 3.8152 -- 138 2615 0.1825 0.3075 -- 99.0
X Ray Diffraction 3.8152 41.4047 -- 152 2882 0.1795 0.2054 -- 100.0
RMS Deviations
Key Refinement Restraint Deviation
f_bond_d 0.006
f_chiral_restr 0.054
f_dihedral_angle_d 11.296
f_angle_d 0.845
f_plane_restr 0.005
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1297
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 124

Software

Software
Software Name Purpose
Blu-Ice data collection
XDS data reduction
XSCALE data scaling
PHENIX refinement version: 1.12_2829