X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 7.5
Details HANGING DROP. 100MM TRIS PH 7.5, 200MM MG-FORMATE, 15% PEG 8K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 108.14 α = 90
b = 108.14 β = 90
c = 89.81 γ = 120
Symmetry
Space Group P 31 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
PIXEL DECTRIS PILATUS 6M DYNAMICALLY BENDABLE MIRROR 2012-02-29
Diffraction Radiation
Monochromator Protocol
LN2 COOLED FIXED-EXIT SI(111) MONOCHROMATOR SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SLS BEAMLINE X06SA -- SLS X06SA

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
1.55 46.83 99.5 0.06 -- -- 8.57 -- 88092 -- 2.0 29.16
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)
1.55 1.64 98.0 1.12 -- 1.64 8.62 --

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 1.55 46.827 -- 2.0 -- 87950 4377 99.95 -- 0.1605 0.1583 0.2014 --
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 1.5501 1.5677 -- 136 2705 0.3026 0.2998 -- 99.0
X Ray Diffraction 1.5677 1.5861 -- 157 2764 0.2784 0.3288 -- 100.0
X Ray Diffraction 1.5861 1.6055 -- 126 2763 0.2628 0.2831 -- 100.0
X Ray Diffraction 1.6055 1.6258 -- 134 2784 0.2444 0.2776 -- 100.0
X Ray Diffraction 1.6258 1.6472 -- 136 2754 0.2336 0.2563 -- 100.0
X Ray Diffraction 1.6472 1.6697 -- 130 2769 0.2212 0.2646 -- 100.0
X Ray Diffraction 1.6697 1.6936 -- 150 2802 0.2184 0.2303 -- 100.0
X Ray Diffraction 1.6936 1.7189 -- 136 2774 0.2065 0.2617 -- 100.0
X Ray Diffraction 1.7189 1.7457 -- 147 2769 0.2105 0.2638 -- 100.0
X Ray Diffraction 1.7457 1.7744 -- 148 2762 0.1994 0.2379 -- 100.0
X Ray Diffraction 1.7744 1.805 -- 146 2752 0.1957 0.2397 -- 100.0
X Ray Diffraction 1.805 1.8378 -- 159 2759 0.1889 0.2511 -- 100.0
X Ray Diffraction 1.8378 1.8731 -- 148 2791 0.1807 0.2062 -- 100.0
X Ray Diffraction 1.8731 1.9114 -- 151 2730 0.1767 0.2217 -- 100.0
X Ray Diffraction 1.9114 1.9529 -- 147 2779 0.1836 0.2487 -- 100.0
X Ray Diffraction 1.9529 1.9984 -- 163 2767 0.1808 0.2227 -- 100.0
X Ray Diffraction 1.9984 2.0483 -- 153 2731 0.1791 0.2191 -- 100.0
X Ray Diffraction 2.0483 2.1037 -- 136 2799 0.1737 0.2489 -- 100.0
X Ray Diffraction 2.1037 2.1656 -- 130 2822 0.1643 0.2028 -- 100.0
X Ray Diffraction 2.1656 2.2355 -- 128 2805 0.1669 0.2174 -- 100.0
X Ray Diffraction 2.2355 2.3154 -- 145 2763 0.1582 0.2132 -- 100.0
X Ray Diffraction 2.3154 2.4081 -- 130 2809 0.158 0.222 -- 100.0
X Ray Diffraction 2.4081 2.5177 -- 159 2771 0.16 0.2083 -- 100.0
X Ray Diffraction 2.5177 2.6504 -- 148 2805 0.1625 0.2336 -- 100.0
X Ray Diffraction 2.6504 2.8165 -- 150 2790 0.1696 0.2049 -- 100.0
X Ray Diffraction 2.8165 3.0339 -- 149 2798 0.17 0.2156 -- 100.0
X Ray Diffraction 3.0339 3.3391 -- 148 2832 0.156 0.1914 -- 100.0
X Ray Diffraction 3.3391 3.8221 -- 165 2816 0.1354 0.1625 -- 100.0
X Ray Diffraction 3.8221 4.8147 -- 158 2847 0.1206 0.1523 -- 100.0
X Ray Diffraction 4.8147 46.8487 -- 164 2961 0.1518 0.212 -- 100.0
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 15.935
f_angle_d 1.504
f_plane_restr 0.008
f_chiral_restr 0.078
f_bond_d 0.011
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4288
Nucleic Acid Atoms 531
Heterogen Atoms 32
Solvent Atoms 481

Software

Software
Software Name Purpose
PHENIX refinement version: (PHENIX.REFINE)
XDS data reduction
XDS data scaling
PHENIX phasing