X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7
Temperature 293.15
Details 27% PEG 3350, 0.1 M HEPES pH 7.0 - protein pre-incubated with NiCl2 and BHI medium supernatant.

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 62.34 α = 90
b = 67.24 β = 90
c = 115.21 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
PIXEL DECTRIS PILATUS 6M-F -- 2013-04-26
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID29 0.97901 ESRF ID29

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
1.9 45.72 99.9 -- 0.12 -- 7.3 -- 38955 -- -3.0 --
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)
1.9 2.0 99.9 -- 0.714 2.58 7.1 --

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 1.9 45.72 -- 1.36 -- 38891 1945 99.9 -- 0.16 0.158 0.191 Random selection
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 1.9 1.9475 -- 137 2598 0.2143 0.2534 -- 100.0
X Ray Diffraction 1.9475 2.0002 -- 136 2595 0.1877 0.2116 -- 100.0
X Ray Diffraction 2.0002 2.059 -- 137 2590 0.1747 0.2143 -- 100.0
X Ray Diffraction 2.059 2.1255 -- 137 2614 0.1728 0.2142 -- 100.0
X Ray Diffraction 2.1255 2.2015 -- 137 2593 0.1562 0.2159 -- 100.0
X Ray Diffraction 2.2015 2.2896 -- 138 2628 0.1592 0.2018 -- 100.0
X Ray Diffraction 2.2896 2.3938 -- 138 2625 0.1628 0.2041 -- 100.0
X Ray Diffraction 2.3938 2.52 -- 137 2603 0.1617 0.1864 -- 100.0
X Ray Diffraction 2.52 2.6779 -- 139 2638 0.1641 0.1968 -- 100.0
X Ray Diffraction 2.6779 2.8846 -- 138 2625 0.1571 0.1918 -- 100.0
X Ray Diffraction 2.8846 3.1748 -- 139 2649 0.1558 0.2098 -- 100.0
X Ray Diffraction 3.1748 3.6341 -- 141 2665 0.1422 0.1513 -- 100.0
X Ray Diffraction 3.6341 4.5779 -- 142 2704 0.1346 0.1708 -- 100.0
X Ray Diffraction 4.5779 45.7285 -- 149 2819 0.166 0.188 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 21.7
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 13.627
f_bond_d 0.005
f_plane_restr 0.004
f_angle_d 0.941
f_chiral_restr 0.039
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3708
Nucleic Acid Atoms 0
Heterogen Atoms 92
Solvent Atoms 415

Software

Software
Software Name Purpose
PHENIX refinement version: (PHENIX.REFINE: 1.9_1692)
XDS data reduction
PHASER phasing
Coot model building
XSCALE data scaling