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Crystal structure of Candida auris dihydrofolate reductase in complex with inhibitor 1283 and NADPH
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8CRH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 295 30% PEG 3,350
0.2M LiSO4
0.1M Pipes, pH 6.5
Crystal Properties Matthews coefficient Solvent content 2.56 51.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.623 α = 90 b = 72.224 β = 90 c = 105.442 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 0.92091 NSLS-II 17-ID-2
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 2.13 32.33 100 0.051 0.051 0.998 9.7 1.9 28377
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.13 2.19 100 0.571 0.807 0.408 1.3 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 (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 2.13 32.33 26903 1473 99.96 0.18454 0.18172 0.1913 0.2349 0.2386 RANDOM 48.738
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] -1.22 0.44 0.78
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.008 r_dihedral_angle_2_deg 16.287 r_long_range_B_other 9.112 r_long_range_B_refined 9.109 r_scangle_other 7.533 r_dihedral_angle_1_deg 6.796 r_scbond_it 5.26 r_scbond_other 5.259 r_mcangle_it 4.802 r_mcangle_other 4.801
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.008 r_dihedral_angle_2_deg 16.287 r_long_range_B_other 9.112 r_long_range_B_refined 9.109 r_scangle_other 7.533 r_dihedral_angle_1_deg 6.796 r_scbond_it 5.26 r_scbond_other 5.259 r_mcangle_it 4.802 r_mcangle_other 4.801 r_mcbond_other 3.56 r_mcbond_it 3.558 r_angle_refined_deg 2.511 r_angle_other_deg 0.866 r_chiral_restr 0.128 r_bond_refined_d 0.015 r_gen_planes_refined 0.013 r_bond_other_d 0.001 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 61 Heterogen Atoms 158
Software Software Software Name Purpose REFMAC refinement PHASER phasing autoPROC data reduction autoPROC data scaling