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Crystal structure of HpsO from Cupriavidus pinatubonensis, crystal form 1
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 15-22% PEG4000, 0.2 M ammonium acetate, 0.1 M sodium acetate (pH 5.5)
Crystal Properties Matthews coefficient Solvent content 2.15 42.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.72 α = 90 b = 58.72 β = 90 c = 271.48 γ = 90
Symmetry Space Group I 41 2 2
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 2022-12-09 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 41.56 98.1 1 24.3 15.3 99955
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 0.95
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 41.556 99953 4984 97.834 0.12 0.1191 0.1188 0.1358 0.1351 13.826
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] 0.433 0.433 -0.865
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.425 r_rigid_bond_restr 16.733 r_lrange_it 14.124 r_scbond_it 13.726 r_scbond_other 13.72 r_scangle_it 13.167 r_scangle_other 13.162 r_lrange_other 12.902 r_dihedral_angle_3_deg 11.495 r_dihedral_angle_1_deg 6.636
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.425 r_rigid_bond_restr 16.733 r_lrange_it 14.124 r_scbond_it 13.726 r_scbond_other 13.72 r_scangle_it 13.167 r_scangle_other 13.162 r_lrange_other 12.902 r_dihedral_angle_3_deg 11.495 r_dihedral_angle_1_deg 6.636 r_dihedral_angle_2_deg 6.083 r_mcangle_it 6.079 r_mcangle_other 6.077 r_mcbond_it 4.387 r_mcbond_other 4.381 r_angle_refined_deg 1.786 r_angle_other_deg 0.655 r_nbd_refined 0.28 r_xyhbond_nbd_refined 0.248 r_symmetry_nbd_refined 0.248 r_symmetry_nbd_other 0.193 r_nbd_other 0.188 r_nbtor_refined 0.181 r_symmetry_xyhbond_nbd_refined 0.132 r_chiral_restr 0.106 r_symmetry_nbtor_other 0.077 r_symmetry_xyhbond_nbd_other 0.05 r_bond_refined_d 0.011 r_gen_planes_refined 0.01 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1840 Nucleic Acid Atoms Solvent Atoms 264 Heterogen Atoms 8
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing