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Crystal structure of Candida auris dihydrofolate reductase in complex with inhibitor 1282 and NADPH
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7ZZX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 277 28% PEG 3,350, 0.2M LiSO4, 0.1M Tris pH 8.5
Crystal Properties Matthews coefficient Solvent content 2.3 46.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.323 α = 90 b = 73.567 β = 90 c = 93.376 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 Horizontal pre-focus bimorph mirror & KB bimorph mirrors 2024-08-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 17-ID-2 0.97931 NSLS-II 17-ID-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 1.65 34.22 94.7 0.032 0.045 0.032 0.999 10.6 1.9 50319
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.65 1.68 96.4 0.691 0.977 0.691 0.538 1.1 1.9
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.65 34.22 50273 2614 94.498 0.155 0.1513 0.1558 0.2267 0.2283 RANDOM 30.293
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] -1.11 -0.999 2.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 16.575 r_dihedral_angle_6_deg 16.179 r_dihedral_angle_3_deg 15.122 r_lrange_it 13.244 r_lrange_other 13.023 r_scangle_it 10.212 r_scangle_other 9.889 r_mcangle_other 7.465 r_mcangle_it 7.462 r_scbond_it 7.283
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 16.575 r_dihedral_angle_6_deg 16.179 r_dihedral_angle_3_deg 15.122 r_lrange_it 13.244 r_lrange_other 13.023 r_scangle_it 10.212 r_scangle_other 9.889 r_mcangle_other 7.465 r_mcangle_it 7.462 r_scbond_it 7.283 r_scbond_other 7.06 r_dihedral_angle_1_deg 6.33 r_rigid_bond_restr 5.668 r_mcbond_it 5.395 r_mcbond_other 5.375 r_dihedral_angle_other_2_deg 5.05 r_angle_refined_deg 2.318 r_angle_other_deg 0.796 r_nbd_refined 0.211 r_symmetry_nbd_other 0.2 r_nbtor_refined 0.187 r_xyhbond_nbd_refined 0.183 r_nbd_other 0.17 r_symmetry_xyhbond_nbd_refined 0.134 r_symmetry_nbd_refined 0.127 r_ncsr_local_group_1 0.126 r_chiral_restr 0.119 r_symmetry_nbtor_other 0.092 r_symmetry_xyhbond_nbd_other 0.04 r_bond_refined_d 0.016 r_gen_planes_refined 0.011 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3264 Nucleic Acid Atoms Solvent Atoms 229 Heterogen Atoms 174
Software Software Software Name Purpose REFMAC refinement PHASER phasing AutoProcess data reduction Aimless data scaling