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Crystal structure of 4-hydroxybenzoate-1-hydroxylase from Gelatoporia subvermispora (GsMNX1)
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, SITTING DROP 293 LMB screen from Molecular Dimensions condition G7 (11% PEG 8000, 0.4 M sodium chloride, 0.1 M sodium cacodylate pH 6.2)
Crystal Properties Matthews coefficient Solvent content 2.74 55.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 112.216 α = 90 b = 64.789 β = 93.896 c = 160.1 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS EIGER2 XE 16M 2023-03-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9763 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.824 159.73 92.7 0.184 0.075 0.994 6.5 7.1 57625
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.824 2.108 58.9 1.016 0.434 0.786 1.7 6.3
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 1.824 159.73 57625 2912 56.314 0.181 0.1789 0.1873 0.2246 0.2316 35.651
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] 0.05 -0.395 -0.03 0.034
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.049 r_dihedral_angle_3_deg 15.916 r_dihedral_angle_2_deg 9.78 r_dihedral_angle_1_deg 7.203 r_lrange_it 5.826 r_lrange_other 5.797 r_scangle_it 3.919 r_scangle_other 3.919 r_mcangle_it 3.08 r_mcangle_other 3.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.049 r_dihedral_angle_3_deg 15.916 r_dihedral_angle_2_deg 9.78 r_dihedral_angle_1_deg 7.203 r_lrange_it 5.826 r_lrange_other 5.797 r_scangle_it 3.919 r_scangle_other 3.919 r_mcangle_it 3.08 r_mcangle_other 3.08 r_scbond_it 2.539 r_scbond_other 2.537 r_mcbond_it 1.983 r_mcbond_other 1.982 r_angle_refined_deg 1.555 r_angle_other_deg 0.505 r_nbd_refined 0.208 r_nbd_other 0.194 r_symmetry_nbd_refined 0.193 r_symmetry_nbd_other 0.186 r_nbtor_refined 0.178 r_xyhbond_nbd_refined 0.161 r_symmetry_xyhbond_nbd_refined 0.144 r_ncsr_local_group_1 0.089 r_symmetry_nbtor_other 0.081 r_chiral_restr 0.073 r_symmetry_xyhbond_nbd_other 0.055 r_dihedral_angle_other_2_deg 0.028 r_chiral_restr_other 0.014 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6409 Nucleic Acid Atoms Solvent Atoms 379 Heterogen Atoms 108
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction STARANISO data scaling MOLREP phasing