X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7.7
Temperature 290.0
Details CrpaA.00612.a.A3.PW37710 @35 mg/ml, protein was incubated with 3 mM L-Lysylsulfamoyl Adenosine, then mixed 1:1 with IndexG5opt(g3): 23.41% (w/v) PEG-3350, 0.2 M lithium sulfate, 0.1 M Tris:HCl/NaOH, pH = 7.7: cryoprotected with 20% ethylene glycol. Puck: yoz9-1, tray: 297540g3

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 117.03 α = 90
b = 142.87 β = 90
c = 73.24 γ = 90
Symmetry
Space Group P 21 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
PIXEL DECTRIS PILATUS 6M -- 2018-01-12
Diffraction Radiation
Monochromator Protocol
SI(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON CLSI BEAMLINE 08ID-1 1.033200 CLSI 08ID-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
2.15 46.86 100.0 0.093 -- -- 6.519 -- 67507 -- -- 31.5
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)
2.15 2.21 100.0 0.57 -- 3.29 6.305 --

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 2.15 46.86 -- 1.34 -- 67498 1977 99.95 -- 0.1563 0.1549 0.2039 --
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 2.15 2.2038 -- 140 4636 0.1946 0.2564 0.0 100.0
X Ray Diffraction 2.2038 2.2633 -- 154 4580 0.1805 0.2302 0.0 100.0
X Ray Diffraction 2.2633 2.3299 -- 146 4602 0.1762 0.2514 0.0 100.0
X Ray Diffraction 2.3299 2.4051 -- 153 4631 0.1748 0.2364 0.0 100.0
X Ray Diffraction 2.4051 2.4911 -- 129 4634 0.1685 0.2418 0.0 100.0
X Ray Diffraction 2.4911 2.5908 -- 143 4643 0.1643 0.2184 0.0 100.0
X Ray Diffraction 2.5908 2.7087 -- 166 4625 0.1635 0.2342 0.0 100.0
X Ray Diffraction 2.7087 2.8515 -- 146 4620 0.1694 0.2274 0.0 100.0
X Ray Diffraction 2.8515 3.0301 -- 118 4696 0.1655 0.2132 0.0 100.0
X Ray Diffraction 3.0301 3.2641 -- 143 4663 0.1661 0.2197 0.0 100.0
X Ray Diffraction 3.2641 3.5924 -- 130 4702 0.1541 0.2084 0.0 100.0
X Ray Diffraction 3.5924 4.112 -- 137 4734 0.1383 0.1915 0.0 100.0
X Ray Diffraction 4.112 5.1796 -- 133 4785 0.1211 0.151 0.0 100.0
X Ray Diffraction 5.1796 46.8711 -- 139 4970 0.1585 0.1759 0.0 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 35.8385
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 7958
Nucleic Acid Atoms 0
Heterogen Atoms 97
Solvent Atoms 850

Software

Software
Software Name Purpose
XDS data reduction
XSCALE data scaling
PHASER phasing
PHENIX refinement
PDB_EXTRACT data extraction version: 3.24