X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 8
Temperature 291.0
Details 16% PEG6000, 0.1 M Tris-HCl, 0.2 M LiCl, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 94.28 α = 76.57
b = 97.98 β = 80.71
c = 109.85 γ = 78.91
Symmetry
Space Group P 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
PIXEL DECTRIS PILATUS 6M Compound Refractive Lenses 2013-05-22
Diffraction Radiation
Monochromator Protocol
Double crystal SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON DIAMOND BEAMLINE I04 0.97625 Diamond I04

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
3.07 30 97.4 0.06 -- -- 3.5 -- 67490 -- -3.0 81.195
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)
3.07 3.26 92.6 0.631 -- 2.09 -- --

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 3.075 29.827 -- 1.93 -- 67479 3407 97.6 -- 0.2353 0.2329 0.2803 Random
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 3.0748 3.1187 -- 119 2037 0.3811 0.4057 -- 76.0
X Ray Diffraction 3.1187 3.1652 -- 138 2707 0.3544 0.4638 -- 98.0
X Ray Diffraction 3.1652 3.2146 -- 134 2697 0.3455 0.397 -- 98.0
X Ray Diffraction 3.2146 3.2672 -- 152 2720 0.3343 0.3616 -- 98.0
X Ray Diffraction 3.2672 3.3235 -- 142 2689 0.3207 0.3699 -- 99.0
X Ray Diffraction 3.3235 3.3839 -- 144 2715 0.3128 0.3563 -- 98.0
X Ray Diffraction 3.3839 3.4488 -- 149 2639 0.3013 0.3317 -- 99.0
X Ray Diffraction 3.4488 3.5191 -- 150 2695 0.2873 0.3463 -- 98.0
X Ray Diffraction 3.5191 3.5955 -- 160 2672 0.299 0.3788 -- 98.0
X Ray Diffraction 3.5955 3.679 -- 126 2723 0.2821 0.365 -- 98.0
X Ray Diffraction 3.679 3.7709 -- 123 2739 0.276 0.3423 -- 99.0
X Ray Diffraction 3.7709 3.8726 -- 136 2667 0.2568 0.3772 -- 99.0
X Ray Diffraction 3.8726 3.9863 -- 141 2708 0.2421 0.3057 -- 99.0
X Ray Diffraction 3.9863 4.1147 -- 130 2757 0.2349 0.2877 -- 99.0
X Ray Diffraction 4.1147 4.2613 -- 148 2692 0.2241 0.2759 -- 99.0
X Ray Diffraction 4.2613 4.4314 -- 154 2690 0.2217 0.2683 -- 99.0
X Ray Diffraction 4.4314 4.6324 -- 126 2706 0.2154 0.2623 -- 99.0
X Ray Diffraction 4.6324 4.8756 -- 156 2707 0.214 0.2655 -- 99.0
X Ray Diffraction 4.8756 5.1796 -- 149 2711 0.217 0.2993 -- 99.0
X Ray Diffraction 5.1796 5.5771 -- 144 2687 0.2234 0.2653 -- 99.0
X Ray Diffraction 5.5771 6.134 -- 150 2720 0.2352 0.273 -- 99.0
X Ray Diffraction 6.134 7.0115 -- 152 2686 0.2218 0.2808 -- 99.0
X Ray Diffraction 7.0115 8.796 -- 136 2695 0.1771 0.1973 -- 98.0
X Ray Diffraction 8.796 29.828 -- 148 2613 0.1624 0.1771 -- 96.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 54.2796
RMS Deviations
Key Refinement Restraint Deviation
f_angle_d 0.631
f_chiral_restr 0.042
f_plane_restr 0.002
f_dihedral_angle_d 13.601
f_bond_d 0.002
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 21659
Nucleic Acid Atoms 0
Heterogen Atoms 174
Solvent Atoms 0

Software

Software
Software Name Purpose
XSCALE data scaling
PHENIX refinement version: 1.8.1_1168
PDB_EXTRACT data extraction version: 3.11
GDA data collection
XDS data reduction
XDS data scaling
PHASER phasing