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Crystal structure of DHPS-3-dehydrogenase, HpsN H319A variant from Cupriavidus pinatubonensis in complex with substrate (R-DHPS) 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 2.55 51.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.324 α = 90 b = 75.809 β = 117.099 c = 84.674 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 2024-07-05 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 2.01 43.82 99.4 1 7.6 3.9 62003
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 2.01 2.06 0.61 1.2
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 2.013 42.299 61984 2921 99.397 0.168 0.1665 0.176 0.1936 0.2002 29.161
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] 0.088 -0.403 0.143 0.119
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.701 r_dihedral_angle_3_deg 11.696 r_dihedral_angle_2_deg 6.596 r_dihedral_angle_1_deg 6.215 r_lrange_it 4.911 r_lrange_other 4.841 r_scangle_it 3.732 r_scangle_other 3.724 r_mcangle_it 2.325 r_mcangle_other 2.325
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.701 r_dihedral_angle_3_deg 11.696 r_dihedral_angle_2_deg 6.596 r_dihedral_angle_1_deg 6.215 r_lrange_it 4.911 r_lrange_other 4.841 r_scangle_it 3.732 r_scangle_other 3.724 r_mcangle_it 2.325 r_mcangle_other 2.325 r_scbond_it 2.298 r_scbond_other 2.279 r_mcbond_it 1.532 r_mcbond_other 1.531 r_angle_refined_deg 1.245 r_angle_other_deg 0.443 r_nbd_refined 0.206 r_symmetry_xyhbond_nbd_refined 0.198 r_symmetry_nbd_other 0.182 r_nbtor_refined 0.173 r_nbd_other 0.161 r_xyhbond_nbd_refined 0.144 r_metal_ion_refined 0.125 r_symmetry_nbd_refined 0.102 r_symmetry_nbtor_other 0.075 r_chiral_restr 0.062 r_dihedral_angle_other_2_deg 0.014 r_bond_refined_d 0.004 r_gen_planes_refined 0.004 r_symmetry_xyhbond_nbd_other 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6572 Nucleic Acid Atoms Solvent Atoms 459 Heterogen Atoms 123
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing