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p-hydroxybenzoate 3-monooxygenase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293.15 0.2M Magnesium chloride hexahydrate, 10% (v/v) Ethylene glycol, 0.1M HEPES pH 7.5, 15% (v/v) PEG Smear Medium, 5% (v/v) 2-Propanol
Crystal Properties Matthews coefficient Solvent content 3.25 62.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.74 α = 90 b = 178.03 β = 116.167 c = 89.13 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 125 PIXEL DECTRIS PILATUS3 6M 2022-07-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 11C 0.97942 PAL/PLS 11C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 3.29 29.901 96.94 0.997 14.19 6.8 33249
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.29 3.408 0.861
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3.29 29.901 33249 1663 96.942 0.199 0.1955 0.1906 0.2558 0.2501 75.42
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] 5.163 0.685 -2.78 -2.061
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.03 r_dihedral_angle_4_deg 17.243 r_dihedral_angle_3_deg 16.65 r_lrange_other 8.212 r_lrange_it 8.211 r_scangle_it 7.615 r_scangle_other 7.615 r_dihedral_angle_1_deg 6.198 r_mcangle_other 5.893 r_mcangle_it 5.891
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.03 r_dihedral_angle_4_deg 17.243 r_dihedral_angle_3_deg 16.65 r_lrange_other 8.212 r_lrange_it 8.211 r_scangle_it 7.615 r_scangle_other 7.615 r_dihedral_angle_1_deg 6.198 r_mcangle_other 5.893 r_mcangle_it 5.891 r_scbond_it 5.423 r_scbond_other 5.423 r_mcbond_it 3.936 r_mcbond_other 3.933 r_angle_other_deg 2.374 r_angle_refined_deg 1.908 r_nbd_other 0.375 r_symmetry_nbd_other 0.271 r_nbd_refined 0.243 r_xyhbond_nbd_refined 0.215 r_nbtor_refined 0.205 r_symmetry_nbd_refined 0.181 r_symmetry_xyhbond_nbd_other 0.125 r_chiral_restr 0.102 r_symmetry_nbtor_other 0.083 r_bond_other_d 0.036 r_bond_refined_d 0.016 r_gen_planes_other 0.015 r_gen_planes_refined 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12444 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 159
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHENIX phasing