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Crystal structure of DHPS-3-dehydrogenase, HpsN from Cupriavidus pinatubonensis in complex with NADH
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 7.5 293 HEPES, magnesium chloride, PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.42 49.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.307 α = 90 b = 87.556 β = 90 c = 134.197 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 2023-10-27 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) 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 2.235 44.73 99.7 0.049 0.022 1 12.7 6.7 44738
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 2.24 2.31 1.139 0.512 0.752 1.1
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 2.235 43.896 44674 2261 99.639 0.226 0.2226 0.2805 0.2649 71.98
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] 5.424 -1.048 -4.377
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 13.707 r_dihedral_angle_3_deg 13.322 r_lrange_it 8.967 r_lrange_other 8.967 r_mcangle_it 6.15 r_mcangle_other 6.149 r_dihedral_angle_1_deg 6.132 r_scangle_it 5.891 r_scangle_other 5.89 r_dihedral_angle_2_deg 5.439
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 13.707 r_dihedral_angle_3_deg 13.322 r_lrange_it 8.967 r_lrange_other 8.967 r_mcangle_it 6.15 r_mcangle_other 6.149 r_dihedral_angle_1_deg 6.132 r_scangle_it 5.891 r_scangle_other 5.89 r_dihedral_angle_2_deg 5.439 r_mcbond_it 3.802 r_mcbond_other 3.802 r_scbond_it 3.544 r_scbond_other 3.543 r_angle_refined_deg 0.92 r_angle_other_deg 0.315 r_nbd_other 0.222 r_nbd_refined 0.205 r_symmetry_nbd_other 0.184 r_nbtor_refined 0.174 r_symmetry_xyhbond_nbd_other 0.169 r_xyhbond_nbd_refined 0.161 r_symmetry_xyhbond_nbd_refined 0.097 r_symmetry_nbd_refined 0.091 r_symmetry_nbtor_other 0.076 r_metal_ion_refined 0.064 r_dihedral_angle_other_2_deg 0.05 r_chiral_restr 0.042 r_chiral_restr_other 0.007 r_bond_refined_d 0.003 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6268 Nucleic Acid Atoms Solvent Atoms 82 Heterogen Atoms 90
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing