X-RAY DIFFRACTION Experimental Data & Validation


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Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.5
Temperature 293.0
Details 1.7M Li2SO4, 100mM HEPES, pH 7.5, vapor diffusion, hanging drop, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 104.39 α = 90
b = 128.06 β = 90
c = 76.17 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 -- 2011-07-21
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRF BEAMLINE BL17U 0.97915 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
1.77 40.46 87.4 0.081 -- -- -- 43837 43705 -- -3.0 15.47
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)
1.77 1.82 92.0 0.495 -- 2.82 -- --

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 1.77 40.456 -- 2.0 43837 43704 1312 87.36 -- 0.1659 0.1652 0.1891 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 1.77 1.8409 -- 152 4910 0.2238 0.2746 -- 92.0
X Ray Diffraction 1.8409 1.9247 -- 151 4877 0.1938 0.2446 -- 92.0
X Ray Diffraction 1.9247 2.0261 -- 149 4807 0.1692 0.2018 -- 90.0
X Ray Diffraction 2.0261 2.1531 -- 148 4787 0.1615 0.2013 -- 90.0
X Ray Diffraction 2.1531 2.3193 -- 147 4748 0.1572 0.1846 -- 89.0
X Ray Diffraction 2.3193 2.5527 -- 145 4684 0.158 0.1836 -- 87.0
X Ray Diffraction 2.5527 2.922 -- 142 4601 0.1697 0.1783 -- 85.0
X Ray Diffraction 2.922 3.681 -- 140 4521 0.1538 0.1715 -- 83.0
X Ray Diffraction 3.681 40.467 -- 138 4457 0.1581 0.1722 -- 79.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 20.8433
Anisotropic B[1][1] -5.2029
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 6.6785
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.4756
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 14.081
f_plane_restr 0.004
f_chiral_restr 0.076
f_angle_d 1.114
f_bond_d 0.007
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3009
Nucleic Acid Atoms 0
Heterogen Atoms 10
Solvent Atoms 352

Software

Computing
Computing Package Purpose
ADSC Quantum Data Collection
XDS Data Reduction (intensity integration)
XSCALE 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
Xscale data reduction