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Crystal structure of HpsO from Cupriavidus pinatubonensis, crystal form 3
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 16-20% PEG8000, 0.1 M sodium HEPES (pH 7.0)
Crystal Properties Matthews coefficient Solvent content 2.53 51.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.384 α = 90 b = 119.453 β = 90 c = 132.407 γ = 90
Symmetry Space Group P 21 21 21
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 1.8 47.9 100 1 18.4 6.7 102590
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 1.8 1.83 0.88
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 1.8 44.497 102499 5124 99.962 0.181 0.1791 0.1905 0.213 0.1954 32.129
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] 3.542 -2.238 -1.304
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.184 r_dihedral_angle_3_deg 12.579 r_dihedral_angle_2_deg 7.528 r_dihedral_angle_1_deg 6.617 r_lrange_it 6.159 r_lrange_other 6.113 r_scangle_it 5.396 r_scangle_other 5.396 r_scbond_it 3.683 r_scbond_other 3.683
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.184 r_dihedral_angle_3_deg 12.579 r_dihedral_angle_2_deg 7.528 r_dihedral_angle_1_deg 6.617 r_lrange_it 6.159 r_lrange_other 6.113 r_scangle_it 5.396 r_scangle_other 5.396 r_scbond_it 3.683 r_scbond_other 3.683 r_mcangle_it 3.545 r_mcangle_other 3.545 r_mcbond_it 2.812 r_mcbond_other 2.812 r_angle_refined_deg 1.542 r_angle_other_deg 0.545 r_nbd_other 0.235 r_symmetry_nbd_refined 0.219 r_nbd_refined 0.218 r_symmetry_nbd_other 0.189 r_nbtor_refined 0.174 r_symmetry_xyhbond_nbd_refined 0.153 r_xyhbond_nbd_refined 0.151 r_chiral_restr 0.079 r_symmetry_nbtor_other 0.077 r_chiral_restr_other 0.009 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7205 Nucleic Acid Atoms Solvent Atoms 533 Heterogen Atoms 16
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing