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Crystal structure of HpsO in complex with HAS (hydroxyacetonesulfonate) from Cupriavidus pinatubonensis
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, HANGING DROP 293 0.1 M Tris-HCl (pH 8.0), 0.2 M NaCl or LiCl, 20-22% (w/v) PEG4000
Crystal Properties Matthews coefficient Solvent content 2.1 41.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.121 α = 90 b = 124.8 β = 117.325 c = 51.47 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 2023-07-11 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 1.55 46.783 99.1 1 8.8 3.4 64293
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 1.55 1.58 0.61
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 1.55 46.783 64292 3267 99.074 0.163 0.162 0.174 0.1842 0.1926 33.067
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] -0.658 -0.346 0.767 0.162
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.012 r_dihedral_angle_3_deg 12.317 r_dihedral_angle_1_deg 6.672 r_dihedral_angle_2_deg 5.73 r_lrange_it 4.694 r_lrange_other 4.642 r_scangle_it 2.989 r_scangle_other 2.988 r_scbond_it 1.93 r_scbond_other 1.93
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.012 r_dihedral_angle_3_deg 12.317 r_dihedral_angle_1_deg 6.672 r_dihedral_angle_2_deg 5.73 r_lrange_it 4.694 r_lrange_other 4.642 r_scangle_it 2.989 r_scangle_other 2.988 r_scbond_it 1.93 r_scbond_other 1.93 r_mcangle_it 1.795 r_mcangle_other 1.795 r_angle_refined_deg 1.519 r_mcbond_it 1.213 r_mcbond_other 1.213 r_dihedral_angle_other_2_deg 1.002 r_angle_other_deg 0.539 r_nbd_refined 0.223 r_symmetry_nbd_other 0.188 r_nbtor_refined 0.177 r_symmetry_nbd_refined 0.177 r_nbd_other 0.164 r_symmetry_xyhbond_nbd_refined 0.161 r_xyhbond_nbd_refined 0.125 r_chiral_restr 0.079 r_symmetry_nbtor_other 0.076 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_symmetry_xyhbond_nbd_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3611 Nucleic Acid Atoms Solvent Atoms 206 Heterogen Atoms 122
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing