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E. coli dihydropteroate synthase complexed with an 8-mercaptoguanine derivative: 2-((2-amino-9-methyl-6-oxo-6,9-dihydro-1H-purin-8-yl)thio)acetic acid
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 6.2 281 0.266 M MgCl2
28.5 %(w/v) PEG 6000
0.1 M sodium cacodylate, pH 6.2
Protein at 11.1 mg.mL-1
Co-crystallisation
1:1 (150:150 nL) reservoir:protein
Crystal Properties Matthews coefficient Solvent content 2.59 52.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 95.27 α = 90 b = 84.83 β = 109.23 c = 83.78 γ = 90
Symmetry Space Group C 1 2 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 210 2017-03-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX1 0.95370 Australian Synchrotron MX1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.35 61.72 100 13.5 7.4 26259
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1AJ2 2.35 61.72 24967 1288 99.96 0.19817 0.19582 0.2433 0.2076 RANDOM 35.815
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] 0.6 1.32 0.77 -1.84
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.755 r_dihedral_angle_3_deg 14.201 r_dihedral_angle_4_deg 13.695 r_long_range_B_refined 6.011 r_long_range_B_other 6.01 r_dihedral_angle_1_deg 5.789 r_scangle_other 5.615 r_scbond_it 4.374 r_scbond_other 4.373 r_mcangle_it 4.048
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.755 r_dihedral_angle_3_deg 14.201 r_dihedral_angle_4_deg 13.695 r_long_range_B_refined 6.011 r_long_range_B_other 6.01 r_dihedral_angle_1_deg 5.789 r_scangle_other 5.615 r_scbond_it 4.374 r_scbond_other 4.373 r_mcangle_it 4.048 r_mcangle_other 4.048 r_angle_other_deg 3.722 r_mcbond_it 3.041 r_mcbond_other 3.039 r_angle_refined_deg 1.433 r_chiral_restr 0.075 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_gen_planes_other 0.005 r_bond_other_d 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 3955 Nucleic Acid Atoms Solvent Atoms 106 Heterogen Atoms 35
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing