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Crystal structure of HpsN D352A mutant from Cupriavidus pinatubonensis in complex with NAD+
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 7.5 293 HEPES, magnesium chlroide, PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.42 49.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.784 α = 90 b = 88.348 β = 90 c = 134.11 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 2.228 44.7 99.8 0.086 0.039 1 10.4 6.7 45320
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 2.23 2.3 1.1195 0.533 0.621
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 2.228 44.213 45255 2302 99.793 0.214 0.2119 0.258 0.236 53.069
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] 3.634 -1.191 -2.444
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 12.919 r_dihedral_angle_3_deg 12.667 r_lrange_it 6.216 r_lrange_other 6.209 r_dihedral_angle_1_deg 6.012 r_dihedral_angle_2_deg 4.287 r_scangle_it 4.122 r_scangle_other 4.121 r_mcangle_it 3.921 r_mcangle_other 3.92
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 12.919 r_dihedral_angle_3_deg 12.667 r_lrange_it 6.216 r_lrange_other 6.209 r_dihedral_angle_1_deg 6.012 r_dihedral_angle_2_deg 4.287 r_scangle_it 4.122 r_scangle_other 4.121 r_mcangle_it 3.921 r_mcangle_other 3.92 r_scbond_it 2.404 r_scbond_other 2.403 r_mcbond_it 2.332 r_mcbond_other 2.331 r_angle_refined_deg 0.856 r_angle_other_deg 0.297 r_nbd_refined 0.197 r_symmetry_nbd_other 0.177 r_nbtor_refined 0.171 r_nbd_other 0.162 r_xyhbond_nbd_refined 0.136 r_symmetry_xyhbond_nbd_refined 0.083 r_symmetry_nbtor_other 0.075 r_symmetry_nbd_refined 0.069 r_chiral_restr 0.041 r_chiral_restr_other 0.011 r_symmetry_xyhbond_nbd_other 0.009 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 6317 Nucleic Acid Atoms Solvent Atoms 175 Heterogen Atoms 46
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing