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1.73 Angstrom Resolution Crystal Structure of Dihydropteroate Synthase (folP-SMZ_B27) from Soil Uncultured Bacterium.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1AJ2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 295 Protein: 30.0 mg/ml, 0.25M Sodium chloride, 0.25M Potassium chloride, 0.01M HEPES (pH 7.5);
Screen: 0.2M Potassium citrate, 0.1M MES (pH 6.5), 20% (w/v) PEG 3350;
Cryo: 5% (v/v) PEG 200, paratone.
Crystal Properties Matthews coefficient Solvent content 2.2 52.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 101.822 α = 90 b = 101.822 β = 90 c = 206.137 γ = 120
Symmetry Space Group P 64 2 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 CCD MARMOSAIC 300 mm CCD C(111) 2017-02-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.73 30 99.9 0.072 0.072 0.031 20.7 6 66663 -3 21.9
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.73 1.76 100 0.752 0.752 0.325 0.737 2.6 5.9
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 1AJ2 1.73 29.99 63061 3346 99.84 0.1583 0.15661 0.1705 0.19091 0.2 RANDOM 24.277
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] -0.23 -0.12 -0.23 0.75
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.249 r_dihedral_angle_4_deg 14.279 r_dihedral_angle_3_deg 8.302 r_long_range_B_refined 6.188 r_long_range_B_other 5.836 r_dihedral_angle_1_deg 2.645 r_scangle_other 2.607 r_mcangle_it 1.915 r_mcangle_other 1.915 r_scbond_it 1.631
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.249 r_dihedral_angle_4_deg 14.279 r_dihedral_angle_3_deg 8.302 r_long_range_B_refined 6.188 r_long_range_B_other 5.836 r_dihedral_angle_1_deg 2.645 r_scangle_other 2.607 r_mcangle_it 1.915 r_mcangle_other 1.915 r_scbond_it 1.631 r_scbond_other 1.629 r_angle_refined_deg 1.471 r_mcbond_it 1.158 r_mcbond_other 1.156 r_angle_other_deg 0.879 r_chiral_restr 0.094 r_gen_planes_refined 0.023 r_gen_planes_other 0.02 r_bond_refined_d 0.009 r_bond_other_d 0.001 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 4113 Nucleic Acid Atoms Solvent Atoms 630 Heterogen Atoms 25
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling MOLREP phasing