X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.5
Temperature 293.0
Details 1.7M Li2SO4, 100mM HEPES, 25% PEG3350, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 105.53 α = 90
b = 128.85 β = 90
c = 76.77 γ = 90
Symmetry
Space Group C 2 2 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315 -- 2012-02-17
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRF BEAMLINE BL17U 0.97907 SSRF BL17U

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
2.08 35.32 98.1 -- 0.094 -- 6.6 31388 31388 -- -- 14.77
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)
2.08 2.19 97.9 0.281 0.281 2.2 5.0 4515

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 2.076 35.32 -- 0.0 31388 30975 1562 96.85 -- 0.1735 0.1716 0.2085 --
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 2.0757 2.1427 -- 131 2535 0.1971 0.2378 -- 93.0
X Ray Diffraction 2.1427 2.2193 -- 149 2640 0.1666 0.1825 -- 98.0
X Ray Diffraction 2.2193 2.3081 -- 118 2297 0.1514 0.2221 -- 84.0
X Ray Diffraction 2.3081 2.4132 -- 135 2700 0.1603 0.2023 -- 98.0
X Ray Diffraction 2.4132 2.5403 -- 138 2685 0.1711 0.2164 -- 98.0
X Ray Diffraction 2.5403 2.6995 -- 142 2726 0.1831 0.2558 -- 99.0
X Ray Diffraction 2.6995 2.9078 -- 146 2718 0.2013 0.2541 -- 99.0
X Ray Diffraction 2.9078 3.2002 -- 127 2777 0.1883 0.2349 -- 100.0
X Ray Diffraction 3.2002 3.6629 -- 158 2745 0.1657 0.2056 -- 99.0
X Ray Diffraction 3.6629 4.6133 -- 156 2754 0.1419 0.1695 -- 99.0
X Ray Diffraction 4.6133 35.3248 -- 162 2836 0.1827 0.1997 -- 98.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 20.4473
Anisotropic B[1][1] -5.7888
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 8.1078
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -2.319
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 14.667
f_plane_restr 0.004
f_chiral_restr 0.077
f_angle_d 1.076
f_bond_d 0.007
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3022
Nucleic Acid Atoms 0
Heterogen Atoms 20
Solvent Atoms 243

Software

Computing
Computing Package Purpose
ADSC Quantum Data Collection
XDS Data Reduction (intensity integration)
SCALA Data Reduction (data scaling)
PHASER Structure Solution
PHENIX (phenix.refine: 1.7_650) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.10 data extraction
phenix refinement
Phaser version: 2.3.0 molecular replacement
SCALA version: 3.3.20 data reduction