X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7.4
Temperature 293.0
Details 0.1M MOPS, pH 7.4 0.8M SODIUM CITRATE

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 92.83 α = 90
b = 61.83 β = 102.34
c = 118.72 γ = 90
Symmetry
Space Group C 1 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
PIXEL DECTRIS PILATUS3 6M -- 2018-08-18
Diffraction Radiation
Monochromator Protocol
Double-crystal, Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ALS BEAMLINE 5.0.2 0.97946 ALS 5.0.2

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
2.24 57.99 97.98 0.06679 -- -- 3.2 -- 31810 -- -- 17.04
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)
2.24 2.32 86.12 0.6024 -- 3.02 3.1 --

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 2.24 57.988 -- 1.35 -- 31203 1529 97.98 -- 0.2424 0.2403 0.2817 --
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 2.24 2.3123 -- 132 2311 0.6216 0.5908 0.0 85.0
X Ray Diffraction 2.3123 2.395 -- 145 2670 0.3479 0.3493 0.0 99.0
X Ray Diffraction 2.395 2.4909 -- 134 2733 0.2694 0.3588 0.0 99.0
X Ray Diffraction 2.4909 2.6042 -- 143 2712 0.2585 0.3162 0.0 99.0
X Ray Diffraction 2.6042 2.7415 -- 129 2710 0.2439 0.2778 0.0 98.0
X Ray Diffraction 2.7415 2.9133 -- 134 2764 0.2254 0.2891 0.0 100.0
X Ray Diffraction 2.9133 3.1382 -- 113 2748 0.2328 0.289 0.0 100.0
X Ray Diffraction 3.1382 3.454 -- 155 2733 0.2114 0.2463 0.0 99.0
X Ray Diffraction 3.454 3.9537 -- 155 2701 0.1956 0.255 0.0 98.0
X Ray Diffraction 3.9537 4.9808 -- 134 2762 0.1706 0.1796 0.0 100.0
X Ray Diffraction 4.9808 58.007 -- 155 2830 0.1877 0.2366 0.0 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 34.2087
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 4.004
f_angle_d 0.989
f_bond_d 0.008
f_plane_restr 0.006
f_chiral_restr 0.052
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4081
Nucleic Acid Atoms 0
Heterogen Atoms 45
Solvent Atoms 224

Software

Software
Software Name Purpose
PHENIX refinement version: 1.11.1_2575
Aimless data scaling
PDB_EXTRACT data extraction version: 3.24
MOSFLM data reduction
PHASER phasing