7R4N
Structure of human hydroxyacid oxidase 1 bound with 5-bromo-N-methyl-1H-indazole-3-carboxamide
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 6GMB |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7 | 293 | 0.1 M MIB pH 7; 30% PEG1000 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.36 | 47.93 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 97 | α = 90 |
b = 97 | β = 90 |
c = 80.64 | γ = 90 |
Symmetry | |
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Space Group | I 4 |
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 6M | 2019-07-02 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I04-1 | 0.91587 | 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 | 1.46 | 62.09 | 99.9 | 0.058 | 0.063 | 0.025 | 0.999 | 14.5 | 5.9 | 64629 |
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 | 1.46 | 1.5 | 99.7 | 1.049 | 1.213 | 0.6 | 0.584 | 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 | 6GMB | 1.7 | 62.09 | 38928 | 2116 | 99.88 | 0.1638 | 0.1621 | 0.1938 | RANDOM | 21.377 |
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] | |
-1.19 | -1.19 | 2.39 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 27.895 |
r_dihedral_angle_4_deg | 15.997 |
r_dihedral_angle_3_deg | 12.393 |
r_dihedral_angle_1_deg | 7.062 |
r_angle_refined_deg | 1.796 |
r_angle_other_deg | 1.541 |
r_chiral_restr | 0.091 |
r_bond_refined_d | 0.015 |
r_gen_planes_refined | 0.011 |
r_gen_planes_other | 0.002 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2650 |
Nucleic Acid Atoms | |
Solvent Atoms | 300 |
Heterogen Atoms | 49 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
Aimless | data scaling |
PDB_EXTRACT | data extraction |
XDS | data reduction |
PHASER | phasing |