X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 5
Temperature 293.0
Details 1.0M Ammonium Sulfate, 0.1M Soldium Citrate, pH 5.0, vapor diffusion, hanging drop, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 107.51 α = 90
b = 132.12 β = 90
c = 163.39 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 -- -- 2011-03-21
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
3.06 74.28 96.5 -- 0.094 -- 6.4 43268 43268 -- -- 51.41
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)
3.06 3.22 80.1 0.344 0.344 2.1 3.6 5155

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 3.056 66.061 -- 0.0 43268 41048 2060 91.65 -- 0.1943 0.1918 0.2418 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 3.0564 3.1275 -- 81 1837 0.2754 0.3539 -- 65.0
X Ray Diffraction 3.1275 3.2057 -- 109 2002 0.2618 0.3082 -- 71.0
X Ray Diffraction 3.2057 3.2924 -- 119 2239 0.2411 0.3309 -- 80.0
X Ray Diffraction 3.2924 3.3892 -- 123 2489 0.2139 0.253 -- 88.0
X Ray Diffraction 3.3892 3.4986 -- 136 2569 0.1923 0.2332 -- 92.0
X Ray Diffraction 3.4986 3.6237 -- 140 2641 0.1862 0.256 -- 94.0
X Ray Diffraction 3.6237 3.7687 -- 132 2682 0.1677 0.227 -- 96.0
X Ray Diffraction 3.7687 3.9402 -- 139 2700 0.1547 0.2194 -- 96.0
X Ray Diffraction 3.9402 4.1479 -- 163 2755 0.1427 0.2019 -- 97.0
X Ray Diffraction 4.1479 4.4078 -- 149 2743 0.1486 0.1939 -- 98.0
X Ray Diffraction 4.4078 4.748 -- 146 2803 0.143 0.1701 -- 99.0
X Ray Diffraction 4.748 5.2256 -- 157 2808 0.1754 0.2741 -- 99.0
X Ray Diffraction 5.2256 5.9814 -- 162 2833 0.2126 0.2509 -- 99.0
X Ray Diffraction 5.9814 7.5342 -- 150 2879 0.2058 0.2601 -- 100.0
X Ray Diffraction 7.5342 66.0759 -- 154 3008 0.248 0.2588 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 57.3276
Anisotropic B[1][1] 46.1344
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -19.6634
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -26.471
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 17.667
f_plane_restr 0.005
f_chiral_restr 0.08
f_angle_d 1.278
f_bond_d 0.009
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 8880
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 83

Software

Computing
Computing Package Purpose
ADSC Quantum Data Collection
MOSFLM 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 molecular replacement
SCALA version: 3.3.20 data reduction