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Crystal structure of hydroquinone-2-hydroxylase from Trametes versicolor (TvMNX3)
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 Structure Screen 1+2 from Molecular Dimensions condition E12 (10 % PEG 6000, 5% MPD, 0.1 M HEPES pH 7.5)
Crystal Properties Matthews coefficient Solvent content 2.73 54.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 175.169 α = 90 b = 178.193 β = 129.301 c = 124.721 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 2022-07-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9762 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 2.408 107.884 92.4 0.28 0.134 0.973 4.1 5.2 78277
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 2.408 2.595 73 0.951 0.464 0.648 1.5 5
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.41 107.884 78264 3986 68.732 0.194 0.1918 0.2255 0.2133 26.309
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] -0.863 -0.405 1.032 0.211
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.936 r_dihedral_angle_6_deg 15.874 r_dihedral_angle_2_deg 10.138 r_dihedral_angle_1_deg 7.121 r_lrange_it 6.165 r_lrange_other 6.165 r_scangle_it 3.758 r_scangle_other 3.758 r_mcangle_it 2.981 r_mcangle_other 2.981
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.936 r_dihedral_angle_6_deg 15.874 r_dihedral_angle_2_deg 10.138 r_dihedral_angle_1_deg 7.121 r_lrange_it 6.165 r_lrange_other 6.165 r_scangle_it 3.758 r_scangle_other 3.758 r_mcangle_it 2.981 r_mcangle_other 2.981 r_scbond_it 2.247 r_scbond_other 2.242 r_mcbond_it 1.761 r_mcbond_other 1.761 r_angle_refined_deg 1.491 r_dihedral_angle_other_2_deg 1.06 r_angle_other_deg 0.479 r_symmetry_nbd_refined 0.269 r_nbd_refined 0.211 r_symmetry_nbd_other 0.195 r_nbd_other 0.192 r_nbtor_refined 0.182 r_xyhbond_nbd_refined 0.162 r_symmetry_xyhbond_nbd_refined 0.134 r_symmetry_nbtor_other 0.083 r_ncsr_local_group_5 0.068 r_chiral_restr 0.065 r_ncsr_local_group_6 0.065 r_ncsr_local_group_1 0.064 r_ncsr_local_group_4 0.063 r_ncsr_local_group_2 0.059 r_ncsr_local_group_3 0.057 r_symmetry_xyhbond_nbd_other 0.04 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 18676 Nucleic Acid Atoms Solvent Atoms 421 Heterogen Atoms 212
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction STARANISO data scaling MOLREP phasing