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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)-N-phenylacetamide
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 8.8 281 0.248 M magnesium nitrate
20.3 %(w/v) PEG 8000
0.1 M tris chloride, pH 8.8
Protein at 11.1 mg.mL-1
1:1 (150:150 nL) reservoir:protein
Ligand soaked into crystal (~4 h, ~2 mM)
Crystal Properties Matthews coefficient Solvent content 2.62 53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 95.364 α = 90 b = 85.621 β = 109.67 c = 83.865 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 0.9537 Australian Synchrotron MX1
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 2.25 46.3 98.4 0.19 0.082 0.995 11.3 6.4 29678
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 2.25 2.32 99.5 1.112 0.447 0.865 2.8 7.32
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 2.25 46.3 28201 1465 98.09 0.19846 0.19669 0.2038 0.23162 0.2396 RANDOM 39.806
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] 1.67 1.58 0.23 -2.41
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.827 r_dihedral_angle_3_deg 13.148 r_dihedral_angle_4_deg 13.006 r_long_range_B_refined 5.752 r_long_range_B_other 5.751 r_dihedral_angle_1_deg 5.512 r_scangle_other 3.981 r_angle_other_deg 3.724 r_mcangle_it 3.589 r_mcangle_other 3.589
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.827 r_dihedral_angle_3_deg 13.148 r_dihedral_angle_4_deg 13.006 r_long_range_B_refined 5.752 r_long_range_B_other 5.751 r_dihedral_angle_1_deg 5.512 r_scangle_other 3.981 r_angle_other_deg 3.724 r_mcangle_it 3.589 r_mcangle_other 3.589 r_scbond_it 2.388 r_scbond_other 2.388 r_mcbond_it 2.196 r_mcbond_other 2.19 r_angle_refined_deg 1.411 r_chiral_restr 0.076 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 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 3983 Nucleic Acid Atoms Solvent Atoms 117 Heterogen Atoms 54
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing