5PD6
PanDDA analysis group deposition -- Crystal Structure of BAZ2B after initial refinement with no ligand modelled (structure 62)
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7 | 277 | 30% PEG600 -- 0.1M MES pH 6.0 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.6 | 65.82 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 82.259 | α = 90 |
b = 97.044 | β = 90 |
c = 58.022 | γ = 90 |
Symmetry | |
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Space Group | C 2 2 21 |
Diffraction
Diffraction Experiment | ||||||||||||||
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ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | PIXEL | DECTRIS PILATUS 2M | 2013-03-10 | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I04-1 | 0.9200 | Diamond | I04-1 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | 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 | 2.01 | 29.01 | 98.6 | 0.186 | 0.203 | 0.08 | 0.991 | 8.2 | 5.9 | 15633 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||
1 | 2.01 | 2.06 | 85.8 | 1.27 | 1.412 | 0.602 | 0.696 | 4.9 | 980 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | FOURIER SYNTHESIS | THROUGHOUT | 3G0L | 2.01 | 29.01 | 14502 | 762 | 96.31 | 0.1956 | 0.1936 | 0.2343 | RANDOM | 38.053 |
Temperature Factor Modeling | ||||||
---|---|---|---|---|---|---|
Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
3.07 | -0.62 | -2.46 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 37.142 |
r_dihedral_angle_4_deg | 20.287 |
r_dihedral_angle_3_deg | 12.395 |
r_dihedral_angle_1_deg | 6.446 |
r_mcangle_it | 5.574 |
r_mcbond_other | 4 |
r_mcbond_it | 3.996 |
r_angle_refined_deg | 1.838 |
r_angle_other_deg | 1.107 |
r_chiral_restr | 0.106 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 930 |
Nucleic Acid Atoms | |
Solvent Atoms | 204 |
Heterogen Atoms | 4 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
Aimless | data scaling |
PDB_EXTRACT | data extraction |
XDS | data reduction |
REFMAC | phasing |