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Structure and design of a new pterin site inhibitor of S. aureus HPPK
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1RAO 1RAO, 1CBK experimental model PDB 1CBK 1RAO, 1CBK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293 90mM bis-tris(pH 6.5), 10mM sodium acetate(pH 4.6), 175mM sodium formate, 1.08M sodium malonate, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 1.95 36.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36.79 α = 90 b = 76.566 β = 100.17 c = 51.522 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 315r 2009-09-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.955 Australian Synchrotron MX2
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 1.65 50.7 100 0.11 7.2 33864 33864 1 1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.65 1.74 100 0.447 4.7 7.2 4934
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 1RAO, 1CBK 1.65 42.3 32158 32158 1684 100 0.181 0.17875 0.1774 0.22463 0.2227 RANDOM 14.696
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] 1.38 0.5 -0.73 -0.48
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.448 r_dihedral_angle_4_deg 18.582 r_dihedral_angle_3_deg 15.055 r_dihedral_angle_1_deg 6.293 r_scangle_it 4.229 r_scbond_it 2.948 r_angle_refined_deg 2.156 r_mcangle_it 2.075 r_mcbond_it 1.33 r_chiral_restr 0.152
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.448 r_dihedral_angle_4_deg 18.582 r_dihedral_angle_3_deg 15.055 r_dihedral_angle_1_deg 6.293 r_scangle_it 4.229 r_scbond_it 2.948 r_angle_refined_deg 2.156 r_mcangle_it 2.075 r_mcbond_it 1.33 r_chiral_restr 0.152 r_bond_refined_d 0.024 r_gen_planes_refined 0.012 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2562 Nucleic Acid Atoms Solvent Atoms 254 Heterogen Atoms 24
Software Software Software Name Purpose Blu-Ice data collection PHASER phasing REFMAC refinement MOSFLM data reduction SCALA data scaling