6V3W
Human Poly(ADP-Ribose) Polymerase 12, Catalytic fragment with four point mutations in complex with RBN-2397
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 4 | 291.15 | 0.2 M Ammonium acetate, 0.1 M Sodium acetate pH 4, 15% w/v PEG 4000 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.95 | 58.27 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 80.466 | α = 90 |
b = 80.466 | β = 90 |
c = 142.648 | γ = 120 |
Symmetry | |
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Space Group | P 65 2 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 | 63 | PIXEL | DECTRIS EIGER2 X 16M | 2018-07-13 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SSRF BEAMLINE BL17U1 | 0.97918 | SSRF | BL17U1 |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 2.04 | 69.78 | 99.2 | 0.093 | 0.096 | 0.022 | 0.998 | 18.8 | 19.3 | 18026 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 2.04 | 2.15 | 98.3 | 1.636 | 1.681 | 0.384 | 0.903 | 18.8 |
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 | MOLECULAR REPLACEMENT | THROUGHOUT | 2PQF | 2.04 | 69.78 | 17084 | 918 | 98.84 | 0.2127 | 0.2104 | 0.2553 | RANDOM | 61.258 |
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] | |
0.97 | 0.49 | 0.97 | -3.16 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 34.462 |
r_dihedral_angle_4_deg | 27.99 |
r_dihedral_angle_3_deg | 15.241 |
r_dihedral_angle_1_deg | 7.106 |
r_angle_refined_deg | 1.592 |
r_angle_other_deg | 1.353 |
r_chiral_restr | 0.071 |
r_bond_refined_d | 0.01 |
r_gen_planes_refined | 0.009 |
r_gen_planes_other | 0.003 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1497 |
Nucleic Acid Atoms | |
Solvent Atoms | 49 |
Heterogen Atoms | 37 |
Software
Software | |
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Software Name | Purpose |
Aimless | data scaling |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
XDS | data reduction |
REFMAC | phasing |