X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8
Temperature 293.0
Details 100 mM Imidazole pH 8.0, 0.8 M NaH2PO4, and 0.55-0.8 M KH2PO4

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 106.11 α = 90
b = 106.11 β = 90
c = 74.79 γ = 90
Symmetry
Space Group P 41

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
PIXEL DECTRIS PILATUS3 6M -- 2017-11-29
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 24-ID-C 0.9792 APS 24-ID-C

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
2.14 106.11 99.3 0.064 -- -- 6.6 -- 45579 -- -- --
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)
2.14 2.2 91.5 1.402 -- 1.2 6.5 --

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
SAD 2.141 61.13 -- 1.34 -- 45519 2289 99.19 -- 0.2041 0.2025 0.2326 --
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 2.1408 2.1874 -- 104 2380 0.2983 0.2976 -- 88.0
X Ray Diffraction 2.1874 2.2383 -- 150 2739 0.2851 0.2994 -- 100.0
X Ray Diffraction 2.2383 2.2943 -- 152 2671 0.2723 0.3133 -- 100.0
X Ray Diffraction 2.2943 2.3563 -- 150 2714 0.2612 0.2885 -- 100.0
X Ray Diffraction 2.3563 2.4256 -- 148 2680 0.2526 0.2648 -- 100.0
X Ray Diffraction 2.4256 2.5039 -- 155 2718 0.2443 0.273 -- 100.0
X Ray Diffraction 2.5039 2.5934 -- 153 2709 0.2437 0.314 -- 100.0
X Ray Diffraction 2.5934 2.6973 -- 123 2724 0.2474 0.2798 -- 100.0
X Ray Diffraction 2.6973 2.82 -- 125 2734 0.2467 0.308 -- 100.0
X Ray Diffraction 2.82 2.9687 -- 132 2714 0.2619 0.2844 -- 100.0
X Ray Diffraction 2.9687 3.1547 -- 132 2748 0.2352 0.3024 -- 100.0
X Ray Diffraction 3.1547 3.3982 -- 128 2738 0.2168 0.2421 -- 100.0
X Ray Diffraction 3.3982 3.7402 -- 164 2709 0.198 0.234 -- 100.0
X Ray Diffraction 3.7402 4.2813 -- 143 2732 0.167 0.192 -- 100.0
X Ray Diffraction 4.2813 5.3934 -- 144 2778 0.1607 0.1827 -- 100.0
X Ray Diffraction 5.3934 61.1548 -- 186 2742 0.1944 0.2201 -- 100.0
RMS Deviations
Key Refinement Restraint Deviation
f_chiral_restr 0.04
f_bond_d 0.003
f_angle_d 0.566
f_plane_restr 0.003
f_dihedral_angle_d 11.027
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 5207
Nucleic Acid Atoms 0
Heterogen Atoms 10
Solvent Atoms 152

Software

Software
Software Name Purpose
PHENIX refinement version: (1.15.2_3472: ???)
XDS data reduction
Aimless data scaling
PHENIX phasing