X-RAY DIFFRACTION Experimental Data & Validation


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Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 4.5
Temperature 289.0
Details 100mM sodium acetate, 2.9-3.3M sodium chloride, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 107.69 α = 90
b = 122.38 β = 90
c = 404.66 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315 -- 2012-03-04
Diffraction Radiation
Monochromator Protocol
double crystal SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRF BEAMLINE BL17U 0.979150 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
2.9 50 100.0 0.138 -- -- 7.2 117324 117324 -- -- --
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)
2.9 3.0 100.0 0.703 -- -- 7.2 11557

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
FOURIER SYNTHESIS 2.913 49.287 -- 1.34 -- 117178 2115 99.57 -- 0.2531 0.2528 0.2685 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 2.9134 2.9812 -- 142 7104 0.3843 0.3732 -- 94.0
X Ray Diffraction 2.9812 3.0557 -- 135 7592 0.3633 0.384 -- 100.0
X Ray Diffraction 3.0557 3.1383 -- 140 7630 0.3477 0.3447 -- 100.0
X Ray Diffraction 3.1383 3.2307 -- 140 7604 0.3356 0.369 -- 100.0
X Ray Diffraction 3.2307 3.3349 -- 141 7624 0.3101 0.3518 -- 100.0
X Ray Diffraction 3.3349 3.4541 -- 138 7640 0.2949 0.2997 -- 100.0
X Ray Diffraction 3.4541 3.5924 -- 138 7675 0.2827 0.31 -- 100.0
X Ray Diffraction 3.5924 3.7558 -- 138 7630 0.2621 0.2744 -- 100.0
X Ray Diffraction 3.7558 3.9537 -- 139 7692 0.2493 0.2362 -- 100.0
X Ray Diffraction 3.9537 4.2013 -- 144 7663 0.2246 0.2156 -- 100.0
X Ray Diffraction 4.2013 4.5255 -- 142 7743 0.2096 0.2219 -- 100.0
X Ray Diffraction 4.5255 4.9805 -- 141 7709 0.1983 0.2043 -- 100.0
X Ray Diffraction 4.9805 5.7003 -- 140 7788 0.231 0.2733 -- 100.0
X Ray Diffraction 5.7003 7.1782 -- 146 7860 0.2367 0.2744 -- 100.0
X Ray Diffraction 7.1782 49.2938 -- 151 8109 0.2298 0.2455 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 76.8921
Anisotropic B[1][1] 18.747
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -3.2561
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -15.491
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 9.495
f_plane_restr 0.001
f_chiral_restr 0.033
f_angle_d 0.463
f_bond_d 0.002
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 22127
Nucleic Acid Atoms 0
Heterogen Atoms 156
Solvent Atoms 0

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
PHENIX (phenix.refine: 1.7_650) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
phenix refinement
SCALEPACK data reduction