7D0Q
Crystal structure of human HBO1-BRPF2 in complex with butyryl-coenzyme A
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 5GK9 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 289 | 0.1 M Tris, pH 8.5, 20% w/v PEG 6000 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.42 | 49.19 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 126.871 | α = 90 |
b = 39.599 | β = 122.89 |
c = 87.9 | γ = 90 |
Symmetry | |
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Space Group | C 1 2 1 |
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 PILATUS3 6M | 2018-04-16 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SSRF BEAMLINE BL19U1 | 0.97892 | SSRF | BL19U1 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | 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 | 2.2 | 50.01 | 99.3 | 0.09 | 1 | 28.6 | 6.6 | 18377 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 2.2 | 2.28 | 0.56 | 0.95 | 2.4 |
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 | 5GK9 | 2.21 | 50.01 | 17452 | 925 | 98.2 | 0.1889 | 0.186 | 0.2435 | RANDOM | 69.279 |
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] | |
-2.87 | -0.9 | 2.39 | 0.89 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 39.867 |
r_sphericity_bonded | 37.881 |
r_sphericity_free | 35.277 |
r_dihedral_angle_4_deg | 21.888 |
r_dihedral_angle_3_deg | 17.598 |
r_rigid_bond_restr | 7.768 |
r_dihedral_angle_1_deg | 6.035 |
r_angle_refined_deg | 1.212 |
r_chiral_restr | 0.059 |
r_bond_refined_d | 0.007 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2480 |
Nucleic Acid Atoms | |
Solvent Atoms | 54 |
Heterogen Atoms | 59 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
HKL-3000 | data scaling |
PDB_EXTRACT | data extraction |
HKL-3000 | data reduction |
PHENIX | phasing |