X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.4
Temperature 293.0
Details 0.1 M sodium cacodylate, pH 6.4, 0.2 M magnesium chloride, 17% PEG8000, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 124.41 α = 90
b = 124.41 β = 90
c = 147.47 γ = 120
Symmetry
Space Group P 31

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
PIXEL DECTRIS PILATUS 6M -- 2012-10-09
Diffraction Radiation
Monochromator Protocol
double crystal Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SLS BEAMLINE X10SA 0.9793 SLS X10SA

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
2.7 49.16 100.0 0.094 -- -- -- -- 70034 0.0 -3.0 56.958
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)
2.7 2.8 100.0 0.717 -- 3.67 -- --

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 2.701 49.157 -- 1.99 -- 69987 3499 99.91 -- 0.2191 0.2174 0.2486 --
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 2.701 2.7377 -- 138 2620 0.2999 0.3708 -- 100.0
X Ray Diffraction 2.7377 2.7768 -- 142 2709 0.3134 0.3801 -- 100.0
X Ray Diffraction 2.7768 2.8183 -- 139 2630 0.3074 0.297 -- 100.0
X Ray Diffraction 2.8183 2.8623 -- 141 2675 0.306 0.3312 -- 100.0
X Ray Diffraction 2.8623 2.9092 -- 140 2674 0.2858 0.318 -- 100.0
X Ray Diffraction 2.9092 2.9594 -- 141 2667 0.2923 0.3062 -- 100.0
X Ray Diffraction 2.9594 3.0132 -- 140 2667 0.28 0.2861 -- 100.0
X Ray Diffraction 3.0132 3.0711 -- 140 2658 0.2773 0.2838 -- 100.0
X Ray Diffraction 3.0711 3.1338 -- 140 2656 0.283 0.2899 -- 100.0
X Ray Diffraction 3.1338 3.2019 -- 140 2657 0.2717 0.3039 -- 100.0
X Ray Diffraction 3.2019 3.2764 -- 141 2675 0.2675 0.2986 -- 100.0
X Ray Diffraction 3.2764 3.3583 -- 139 2634 0.255 0.314 -- 100.0
X Ray Diffraction 3.3583 3.4491 -- 141 2688 0.2432 0.2728 -- 100.0
X Ray Diffraction 3.4491 3.5506 -- 139 2642 0.2318 0.2553 -- 100.0
X Ray Diffraction 3.5506 3.6651 -- 139 2631 0.2217 0.2639 -- 100.0
X Ray Diffraction 3.6651 3.7961 -- 141 2695 0.2294 0.2438 -- 100.0
X Ray Diffraction 3.7961 3.948 -- 139 2641 0.2015 0.2614 -- 100.0
X Ray Diffraction 3.948 4.1276 -- 140 2663 0.1816 0.1968 -- 100.0
X Ray Diffraction 4.1276 4.3451 -- 140 2657 0.1733 0.2063 -- 100.0
X Ray Diffraction 4.3451 4.6171 -- 141 2684 0.1721 0.2043 -- 100.0
X Ray Diffraction 4.6171 4.9733 -- 140 2670 0.1798 0.1952 -- 100.0
X Ray Diffraction 4.9733 5.4732 -- 140 2647 0.1907 0.2246 -- 100.0
X Ray Diffraction 5.4732 6.2638 -- 139 2651 0.2009 0.252 -- 100.0
X Ray Diffraction 6.2638 7.8865 -- 140 2659 0.2039 0.2489 -- 100.0
X Ray Diffraction 7.8865 49.1648 -- 139 2638 0.1715 0.195 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 50.3913
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.004
f_chiral_restr 0.07
f_dihedral_angle_d 16.984
f_angle_d 1.057
f_bond_d 0.014
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 13990
Nucleic Acid Atoms 0
Heterogen Atoms 174
Solvent Atoms 146

Software

Computing
Computing Package Purpose
XDS Data Collection
XSCALE Data Reduction (intensity integration)
XSCALE Data Reduction (data scaling)
PHASER MR Structure Solution
PHENIX (phenix.refine: 1.8.1_1168) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
phenix refinement
Xscale data reduction