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Crystal structure of HpsO from Cupriavidus pinatubonensis, crystal form 2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold AF-Q46N54-F1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 20 - 22% PEG4000, 0.2 M sodium chloride or lithium chloride, 0.1 M Tris-HCl (pH 8.0)
Crystal Properties Matthews coefficient Solvent content 2.05 39.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.684 α = 90 b = 122.176 β = 117.099 c = 51.314 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 EIGER X 16M 2023-03-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.9537 Australian Synchrotron MX2
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 1.08 37.51 99.3 1 13.3 3.4 184643
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 1.08 1.11 0.91
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 1.08 37.509 184642 9472 99.23 0.118 0.1175 0.1173 0.1349 0.1345 11.698
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] -0.003 -0.078 0.029 0.036
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.621 r_dihedral_angle_3_deg 12.127 r_lrange_it 12.033 r_lrange_other 11.156 r_dihedral_angle_2_deg 10.558 r_scangle_it 7.891 r_scangle_other 7.89 r_mcangle_it 7.338 r_mcangle_other 7.337 r_dihedral_angle_1_deg 6.548
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.621 r_dihedral_angle_3_deg 12.127 r_lrange_it 12.033 r_lrange_other 11.156 r_dihedral_angle_2_deg 10.558 r_scangle_it 7.891 r_scangle_other 7.89 r_mcangle_it 7.338 r_mcangle_other 7.337 r_dihedral_angle_1_deg 6.548 r_mcbond_it 6.23 r_mcbond_other 6.229 r_scbond_it 5.321 r_scbond_other 5.32 r_rigid_bond_restr 4.114 r_angle_refined_deg 1.813 r_angle_other_deg 0.655 r_nbd_refined 0.376 r_symmetry_nbd_other 0.24 r_symmetry_xyhbond_nbd_refined 0.233 r_nbtor_refined 0.205 r_nbd_other 0.175 r_xyhbond_nbd_refined 0.159 r_symmetry_nbd_refined 0.118 r_chiral_restr 0.102 r_symmetry_nbtor_other 0.079 r_bond_refined_d 0.01 r_gen_planes_refined 0.01 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3582 Nucleic Acid Atoms Solvent Atoms 408 Heterogen Atoms 8
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing