4CY6
apo structure of 2-hydroxybiphenyl 3-monooxygenase HbpA
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3IHG | PDB ENTRIES 3IHG |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 5.5 | 18% (W/V) PEG 3350, 0.15 M KSCN IN BIS-TRIS PROPANE BUFFER AT PH 5.5, WITH A PROTEIN CONCENTRATION OF 10 MG ML-1. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.54 | 51.5 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 79.35 | α = 115.03 |
b = 94.67 | β = 96.09 |
c = 99.16 | γ = 109.59 |
Symmetry | |
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Space Group | P 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 | 120 | PIXEL | DECTRIS PILATUS 6M | 2012-12-02 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I04 | Diamond | I04 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge 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 | 2.76 | 85.97 | 97.9 | 0.1 | 5.4 | 2.1 | 59321 | 2 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 2.76 | 2.83 | 97.8 | 0.48 | 1.6 | 2 |
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 | PDB ENTRIES 3IHG | 2.76 | 85.97 | 55716 | 2967 | 96.81 | 0.19262 | 0.19 | 0.24114 | RANDOM | 59.665 |
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] | |
-4.73 | 1.03 | 0.24 | 2.57 | 2.13 | -1.44 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 34.281 |
r_dihedral_angle_4_deg | 19.787 |
r_dihedral_angle_3_deg | 17.59 |
r_dihedral_angle_1_deg | 7.466 |
r_mcangle_it | 7.396 |
r_scbond_it | 5.621 |
r_mcbond_it | 5.136 |
r_mcbond_other | 5.136 |
r_angle_refined_deg | 1.626 |
r_angle_other_deg | 1.061 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 16126 |
Nucleic Acid Atoms | |
Solvent Atoms | 139 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
xia2 | data reduction |
SCALA | data scaling |
BALBES | phasing |