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Crystal structure of Candida auris dihydrofolate reductase in complex with inhibitor 1172 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 8.5 295 30% PEG3,350
0.2M LiSO4
0.1M Tris, pH 8.5
Crystal Properties Matthews coefficient Solvent content 2.61 52.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.146 α = 90 b = 72.337 β = 90 c = 104.909 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 9M KB bimorph mirrors 2024-04-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 17-ID-1 0.92010 NSLS-II 17-ID-1
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 1.98 29.72 99.8 0.084 0.088 0.024 0.999 19 13.4 35202
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 1.98 2.03 98.1 0.8 0.835 0.237 0.848 12.3
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 (Observed) 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 1.98 29.72 33442 1703 99.84 0.17076 0.16768 0.18 0.23279 0.2404 RANDOM 43.656
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] 0.22 0.19 -0.41
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.406 r_dihedral_angle_2_deg 13.288 r_long_range_B_other 11.203 r_long_range_B_refined 11.2 r_scangle_other 9.611 r_dihedral_angle_1_deg 7.64 r_scbond_it 7.269 r_scbond_other 7.135 r_mcangle_it 6.384 r_mcangle_other 6.382
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.406 r_dihedral_angle_2_deg 13.288 r_long_range_B_other 11.203 r_long_range_B_refined 11.2 r_scangle_other 9.611 r_dihedral_angle_1_deg 7.64 r_scbond_it 7.269 r_scbond_other 7.135 r_mcangle_it 6.384 r_mcangle_other 6.382 r_mcbond_it 5.4 r_mcbond_other 5.396 r_angle_refined_deg 2.612 r_angle_other_deg 0.875 r_chiral_restr 0.143 r_bond_refined_d 0.015 r_gen_planes_refined 0.015 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_dihedral_angle_4_deg r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3264 Nucleic Acid Atoms Solvent Atoms 191 Heterogen Atoms 185
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PHASER phasing XDS data reduction