X-RAY DIFFRACTION Experimental Data & Validation


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Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 5.5
Temperature 281.0
Details 0.1M tri-sodium citrate pH 5.5, 20% PEG 3000, VAPOR DIFFUSION, SITTING DROP, temperature 281K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 46.36 α = 70.49
b = 62.69 β = 86.93
c = 83.12 γ = 79.1
Symmetry
Space Group P 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315 -- --
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.9184 AUSTRALIAN SYNCHROTRON MX2

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
2.5 -- 97.3 -- -- -- -- -- 25246 -- -- 20.76
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)
2.5 2.64 97.6 0.233 -- 5.6 5.9 --

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
MIR 2.5 19.768 -- 1.97 -- 29147 1452 97.44 -- 0.1914 0.1893 0.232 --
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 2.5 2.5892 -- 171 2765 0.2353 0.3193 -- 97.0
X Ray Diffraction 2.5892 2.6926 -- 151 2746 0.2186 0.2916 -- 98.0
X Ray Diffraction 2.6926 2.8148 -- 139 2811 0.2193 0.256 -- 98.0
X Ray Diffraction 2.8148 2.9628 -- 131 2811 0.2029 0.2574 -- 98.0
X Ray Diffraction 2.9628 3.1477 -- 136 2780 0.2028 0.2504 -- 98.0
X Ray Diffraction 3.1477 3.3896 -- 148 2780 0.1921 0.2539 -- 98.0
X Ray Diffraction 3.3896 3.7287 -- 152 2786 0.1828 0.2073 -- 98.0
X Ray Diffraction 3.7287 4.2635 -- 143 2775 0.1647 0.2012 -- 97.0
X Ray Diffraction 4.2635 5.3538 -- 121 2763 0.1548 0.1961 -- 97.0
X Ray Diffraction 5.3538 19.7682 -- 160 2678 0.194 0.2028 -- 95.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 22.5707
Anisotropic B[1][1] 10.6682
Anisotropic B[1][2] -6.6771
Anisotropic B[1][3] 15.5774
Anisotropic B[2][2] -4.5816
Anisotropic B[2][3] -5.2056
Anisotropic B[3][3] 3.6649
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.005
f_chiral_restr 0.115
f_dihedral_angle_d 14.384
f_angle_d 1.382
f_bond_d 0.006
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 7007
Nucleic Acid Atoms 0
Heterogen Atoms 69
Solvent Atoms 326

Software

Computing
Computing Package Purpose
blueice Data Collection
XDS Data Reduction (intensity integration)
SCALA Data Reduction (data scaling)
PHENIX Structure Solution
PHENIX (phenix.refine: 1.7.1_743) Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine: 1.7.1_743) refinement
PHENIX model building
blueice data collection