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 (PILATUS 6M) DECTRIS 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
OTHER 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_plane_restr 0.008
f_chiral_restr 0.078
f_dihedral_angle_d 15.935
f_angle_d 1.504
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

Computing
Computing Package Purpose
XDS Data Reduction (intensity integration)
XDS Data Reduction (data scaling)
PHENIX Structure Solution
PHENIX (PHENIX.REFINE) Structure Refinement
Software
Software Name Purpose
PHENIX version: (PHENIX.REFINE) refinement
PHENIX model building