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Crystal structure of DHPS-3-dehydrogenase, HpsN from Cupriavidus pinatubonensis in complex with product analogue (L-cysteate) and NADH
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold AF-Q46N53-F1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 PEG 3350, BIS-TRIS, lithium sulfate
Crystal Properties Matthews coefficient Solvent content 2.56 51.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.931 α = 90 b = 76.339 β = 117.038 c = 85.076 γ = 90
Symmetry Space Group P 1 21 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 2024-06-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.95372 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 1.75 43.898 99.2 1 10.6 2.9 94390
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 1.75 1.78 0.74 1.7
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 1.751 43.898 94368 4773 99.088 0.149 0.1477 0.1593 0.1774 0.1886 22.437
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] -0.21 -0.115 0.57 -0.159
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.232 r_dihedral_angle_3_deg 10.876 r_dihedral_angle_2_deg 7.38 r_dihedral_angle_1_deg 6.064 r_lrange_it 5.242 r_lrange_other 5.12 r_scangle_it 4.306 r_scangle_other 4.306 r_scbond_other 2.696 r_scbond_it 2.695
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.232 r_dihedral_angle_3_deg 10.876 r_dihedral_angle_2_deg 7.38 r_dihedral_angle_1_deg 6.064 r_lrange_it 5.242 r_lrange_other 5.12 r_scangle_it 4.306 r_scangle_other 4.306 r_scbond_other 2.696 r_scbond_it 2.695 r_mcangle_it 2.19 r_mcangle_other 2.19 r_mcbond_it 1.569 r_mcbond_other 1.568 r_angle_refined_deg 1.534 r_angle_other_deg 0.541 r_symmetry_nbd_refined 0.237 r_nbd_refined 0.215 r_nbd_other 0.191 r_symmetry_nbd_other 0.182 r_nbtor_refined 0.176 r_symmetry_xyhbond_nbd_refined 0.152 r_xyhbond_nbd_refined 0.141 r_chiral_restr 0.077 r_symmetry_nbtor_other 0.076 r_metal_ion_refined 0.065 r_dihedral_angle_other_2_deg 0.012 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 r_symmetry_xyhbond_nbd_other 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 6590 Nucleic Acid Atoms Solvent Atoms 627 Heterogen Atoms 110
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing