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Crystal structure of dihydropteroate synthase H182G mutant (folP-SMZ_B27) from soil uncultured bacterium in complex with pteroic acid and pyrophosphate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5VIS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 298 25% (w/v) PEG 3350, 1% DMSO, 0.1 M Hepes pH 7.5, 5 mM para-aminobenzoic acid, 1.2 mM 6-hydroxymethyl-7,8-dihydropterin pyrophosphate
Crystal Properties Matthews coefficient Solvent content 1.98 37.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.167 α = 90 b = 145.614 β = 90 c = 36.801 γ = 90
Symmetry Space Group P 21 21 2
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 PILATUS3 6M 2019-10-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.978 APS 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) 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 1.82 50 98.3 0.136 0.075 16.5 6 42814
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 1.82 1.85 79.5 0.867 0.583 0.982 1.1 2.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 FREE R-VALUE 5VIS 1.82 42.41 1.34 42619 1995 97.7 0.1669 0.1647 0.1644 0.2108 0.2105 RANDOM 33.99
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 16.4685 f_angle_d 0.9417 f_chiral_restr 0.0603 f_plane_restr 0.009 f_bond_d 0.0071
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4086 Nucleic Acid Atoms Solvent Atoms 580 Heterogen Atoms 55
Software Software Software Name Purpose PHENIX refinement HKL-3000 data reduction HKL-3000 data scaling PHENIX phasing PHENIX model building Coot model building