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 1.7 M Li2SO4/100 mM HEPES, pH 7.5, vapor diffusion, hanging drop, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 104.71 α = 90
b = 128.73 β = 90
c = 76.16 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 315r -- 2011-05-12
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
1.5 43.14 99.0 0.064 -- -- -- -- 68706 -- -3.0 22.288
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)
1.5 1.59 98.0 0.582 -- 2.95 -- --

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 1.59 43.144 -- 1.99 81377 68698 2062 99.17 -- 0.1678 0.1674 0.1813 3%
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 1.59 1.627 -- 137 4415 0.2087 0.2274 -- 100.0
X Ray Diffraction 1.627 1.6677 -- 136 4412 0.1947 0.2289 -- 100.0
X Ray Diffraction 1.6677 1.7128 -- 138 4436 0.1876 0.1979 -- 100.0
X Ray Diffraction 1.7128 1.7632 -- 137 4450 0.1857 0.2134 -- 100.0
X Ray Diffraction 1.7632 1.8201 -- 137 4428 0.1777 0.1945 -- 100.0
X Ray Diffraction 1.8201 1.8851 -- 138 4447 0.1682 0.2 -- 100.0
X Ray Diffraction 1.8851 1.9606 -- 137 4424 0.169 0.1902 -- 100.0
X Ray Diffraction 1.9606 2.0499 -- 137 4455 0.1597 0.2336 -- 100.0
X Ray Diffraction 2.0499 2.1579 -- 137 4427 0.1634 0.1762 -- 100.0
X Ray Diffraction 2.1579 2.2931 -- 138 4458 0.1586 0.1773 -- 100.0
X Ray Diffraction 2.2931 2.4702 -- 137 4435 0.1696 0.1811 -- 99.0
X Ray Diffraction 2.4702 2.7187 -- 139 4470 0.1758 0.1881 -- 99.0
X Ray Diffraction 2.7187 3.112 -- 137 4448 0.1774 0.1868 -- 99.0
X Ray Diffraction 3.112 3.9204 -- 138 4457 0.1528 0.1533 -- 98.0
X Ray Diffraction 3.9204 43.1599 -- 139 4474 0.1579 0.1581 -- 95.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 19.2606
Anisotropic B[1][1] -4.8439
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 6.9487
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -2.1047
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 12.226
f_plane_restr 0.005
f_chiral_restr 0.076
f_angle_d 1.118
f_bond_d 0.006
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2974
Nucleic Acid Atoms 0
Heterogen Atoms 26
Solvent Atoms 462

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: 3.11 data extraction
phenix refinement
Xscale data reduction