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Crystal structure of the 3-dehydroquinate synthase (DHQS) domain of Aro1 from Candida albicans SC5314 in complex with NADH
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1SG6 PDB entry 1SG6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 295 0.2 M sodium thiocyanate, 20% PEG3350, 2 mM NADH, 0.5 mM zinc chloride, cryoprotectant: 8% glycerol, 8% ethylene glycol, 8% sucrose
Crystal Properties Matthews coefficient Solvent content 2.4 48.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.678 α = 90 b = 92.06 β = 97.57 c = 88.915 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 CCD ADSC QUANTUM 210r mirrors 2017-12-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-BM 0.9793 APS 19-BM
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.85 30 99.9 0.045 37.8 4.8 69649 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.85 1.88 100 0.956 0.717 1.44 3.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 PDB entry 1SG6 1.85 30 66446 2108 99.26 0.17695 0.17606 0.1839 0.203 0.2074 RANDOM 41.338
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 1.23 -1.3 -1.96
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.441 r_dihedral_angle_4_deg 15.611 r_dihedral_angle_3_deg 14.11 r_dihedral_angle_1_deg 5.702 r_long_range_B_refined 5.392 r_long_range_B_other 5.392 r_angle_refined_deg 1.655 r_scangle_other 1.374 r_angle_other_deg 0.99 r_mcangle_it 0.939
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.441 r_dihedral_angle_4_deg 15.611 r_dihedral_angle_3_deg 14.11 r_dihedral_angle_1_deg 5.702 r_long_range_B_refined 5.392 r_long_range_B_other 5.392 r_angle_refined_deg 1.655 r_scangle_other 1.374 r_angle_other_deg 0.99 r_mcangle_it 0.939 r_mcangle_other 0.939 r_scbond_it 0.931 r_scbond_other 0.929 r_mcbond_it 0.602 r_mcbond_other 0.601 r_chiral_restr 0.094 r_bond_refined_d 0.014 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 5908 Nucleic Acid Atoms Solvent Atoms 389 Heterogen Atoms 141
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling PHASER phasing SBC-Collect data collection