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apo structure of 2-hydroxybiphenyl 3-monooxygenase HbpA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3IHG PDB ENTRIES 3IHG
Crystallization Crystalization Experiments 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 Matthews coefficient Solvent content 2.54 51.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.35 α = 115.03 b = 94.67 β = 96.09 c = 99.16 γ = 109.59
Diffraction Diffraction Experiment 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 ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 Diamond I04
Data Collection Overall 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 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 (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) 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 0.1951 0.24114 0.2396 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 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
RMS Deviations 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 r_chiral_restr 0.091 r_bond_refined_d 0.013 r_gen_planes_refined 0.008 r_bond_other_d 0.006 r_gen_planes_other 0.005 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 16126 Nucleic Acid Atoms Solvent Atoms 139 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement xia2 data reduction SCALA data scaling BALBES phasing