X-RAY DIFFRACTION Experimental Data & Validation


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Crystallization

Crystalization Experiments
Method Sitting Drop
pH 6.5
Temperature 298.0
Details 15% PEG 6000, 0.15 M sodium acetate, 0.1M MES buffer, pH 6.5, sitting drop, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 79.18 α = 90
b = 79.18 β = 90
c = 107.89 γ = 120
Symmetry
Space Group P 61 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS IV++ -- --
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU RUH3R 1.54 -- --

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
2.01 42.4 99.5 -- 0.037 -- 5.1 13728 13728 -- -- --
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)
2.014 2.12 98.7 0.118 0.118 5.8 5.1 1918

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 2.014 31.849 -- 0.01 -- 13579 1366 98.41 -- 0.179 0.175 0.213 --
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 2.014 2.086 -- 132 1163 0.189 0.291 -- 96.0
X Ray Diffraction 2.086 2.17 -- 129 1152 0.166 0.191 -- 97.0
X Ray Diffraction 2.17 2.268 -- 133 1194 0.159 0.225 -- 97.0
X Ray Diffraction 2.268 2.388 -- 132 1181 0.166 0.223 -- 98.0
X Ray Diffraction 2.388 2.537 -- 135 1199 0.165 0.211 -- 98.0
X Ray Diffraction 2.537 2.733 -- 136 1224 0.178 0.197 -- 99.0
X Ray Diffraction 2.733 3.008 -- 136 1221 0.176 0.226 -- 99.0
X Ray Diffraction 3.008 3.443 -- 139 1253 0.173 0.207 -- 100.0
X Ray Diffraction 3.443 4.336 -- 142 1268 0.155 0.186 -- 100.0
X Ray Diffraction 4.336 31.853 -- 152 1358 0.179 0.203 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 19.978
Anisotropic B[1][1] -0.782
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.782
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 1.563
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 28.591
f_plane_restr 0.007
f_chiral_restr 0.081
f_angle_d 1.034
f_bond_d 0.005
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1290
Nucleic Acid Atoms 0
Heterogen Atoms 90
Solvent Atoms 171

Software

Computing
Computing Package Purpose
MOSFLM Data Reduction (intensity integration)
SCALA Data Reduction (data scaling)
PHASER Structure Solution
PHENIX (phenix.refine: 1.5_2) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.005 data extraction
phenix refinement
Phaser version: 2.1.1 molecular replacement
SCALA version: 3.3.15 data processing
Mosflm reflection data processing