X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7.5
Temperature 291.0
Details 30% PEG-1500, 0.2M sodium chloride, 0.1M HEPES, pH 7.5, vapor diffusion, sitting drop, temperature 291K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 66.62 α = 90
b = 66.62 β = 90
c = 46.47 γ = 120
Symmetry
Space Group P 63

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
2 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS -- 2010-06-13
CCD ADSC QUANTUM 315 -- 2010-06-17
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 19-ID 0.97904 APS 19-ID
ROTATING ANODE RIGAKU FR-E DW 1.5418 -- --

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
1.3 40 99.8 0.041 -- -- 5.6 -- 28982 -- -- --
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)
1.3 1.32 100.0 0.751 -- -- 5.5 2847

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
SAD 1.3 33.308 -- 0.0 -- 28929 1449 99.807 -- 0.184 0.1839 0.1908 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 1.3 1.334 -- 114 2020 0.217 0.238 -- 99.86
X Ray Diffraction 1.334 1.37 -- 103 1972 0.196 0.221 -- 100.0
X Ray Diffraction 1.37 1.41 -- 131 1877 0.169 0.164 -- 99.801
X Ray Diffraction 1.41 1.453 -- 96 1866 0.166 0.21 -- 99.898
X Ray Diffraction 1.453 1.501 -- 113 1785 0.145 0.165 -- 99.895
X Ray Diffraction 1.501 1.553 -- 84 1745 0.152 0.185 -- 99.836
X Ray Diffraction 1.553 1.612 -- 84 1689 0.155 0.207 -- 99.944
X Ray Diffraction 1.612 1.677 -- 76 1647 0.153 0.151 -- 99.884
X Ray Diffraction 1.677 1.752 -- 75 1565 0.158 0.188 -- 99.939
X Ray Diffraction 1.752 1.837 -- 73 1496 0.159 0.168 -- 99.873
X Ray Diffraction 1.837 1.936 -- 74 1421 0.157 0.206 -- 99.866
X Ray Diffraction 1.936 2.053 -- 60 1337 0.155 0.187 -- 99.857
X Ray Diffraction 2.053 2.194 -- 84 1257 0.155 0.156 -- 99.925
X Ray Diffraction 2.194 2.369 -- 47 1199 0.15 0.122 -- 100.0
X Ray Diffraction 2.369 2.594 -- 55 1093 0.187 0.203 -- 99.739
X Ray Diffraction 2.594 2.898 -- 37 1007 0.2 0.187 -- 99.904
X Ray Diffraction 2.898 3.342 -- 53 856 0.215 0.192 -- 100.0
X Ray Diffraction 3.342 4.083 -- 34 752 0.195 0.199 -- 100.0
X Ray Diffraction 4.083 5.731 -- 35 581 0.196 0.206 -- 99.515
X Ray Diffraction 5.731 33.308 -- 21 315 0.324 0.31 -- 93.333
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 12.991
Anisotropic B[1][1] 0.584
Anisotropic B[1][2] 0.292
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.584
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.876
RMS Deviations
Key Refinement Restraint Deviation
r_scbond_it 3.989
r_chiral_restr 0.11
r_mcbond_other 0.565
r_dihedral_angle_2_deg 36.165
r_dihedral_angle_1_deg 6.733
r_gen_planes_refined 0.008
r_mcangle_it 2.973
r_angle_refined_deg 1.679
r_bond_refined_d 0.018
r_dihedral_angle_3_deg 10.9
r_angle_other_deg 0.921
r_rigid_bond_restr 1.413
r_mcbond_it 1.902
r_bond_other_d 0.002
r_dihedral_angle_4_deg 6.682
r_scangle_it 6.028
r_gen_planes_other 0.001
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 617
Nucleic Acid Atoms 0
Heterogen Atoms 13
Solvent Atoms 69

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
SHELX phasing
REFMAC refinement version: 5.5.0109
PDB_EXTRACT data extraction version: 3.10
SHELXDE phasing