3HKV
Human poly(ADP-ribose) polymerase 10, catalytic fragment in complex with an inhibitor 3-aminobenzamide
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3BLJ | PDB ENTRY 3BLJ |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7.5 | 277 | 0.49M NaH2PO4, 0.9M K2HPO4, pH7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.93 | 58.07 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 97.38 | α = 90 |
b = 97.38 | β = 90 |
c = 121.16 | γ = 90 |
Symmetry | |
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Space Group | P 41 21 2 |
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 | CCD | MARMOSAIC 225 mm CCD | Rh-coated Si mirrors | 2009-03-12 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | MAX II BEAMLINE I911-3 | 0.97900 | MAX II | I911-3 |
Data Collection
Overall | |||||||||||||||||||
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ID # | 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 | 2.1 | 30 | 99.6 | 0.093 | 0.089 | 15.3 | 7.8 | 34589 | 34589 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
2.1 | 2.15 | 99.4 | 0.722 | 0.428 | 4 | 8 | 2499 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB ENTRY 3BLJ | 2.1 | 29.84 | 32856 | 32856 | 1730 | 100 | 0.19801 | 0.19801 | 0.19574 | 0.24196 | RANDOM | 30.7 |
Temperature Factor Modeling | ||||||
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Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
1.05 | 1.05 | -2.1 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 29.76 |
r_dihedral_angle_4_deg | 19.866 |
r_dihedral_angle_3_deg | 16.172 |
r_dihedral_angle_1_deg | 5.882 |
r_scangle_it | 4.628 |
r_scbond_it | 2.691 |
r_mcangle_it | 1.883 |
r_angle_refined_deg | 1.506 |
r_mcbond_it | 0.986 |
r_angle_other_deg | 0.917 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3086 |
Nucleic Acid Atoms | |
Solvent Atoms | 183 |
Heterogen Atoms | 37 |
Software
Software | |
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Software Name | Purpose |
MxCuBE | data collection |
PHASER | phasing |
REFMAC | refinement |
XDS | data reduction |
XSCALE | data scaling |