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The Structure of Dihydropteroate Synthase from Staphylococcus aureus subsp. aureus Mu50.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1AD1 PDB ENTRY 1AD1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 289 0.2M MgCl2, 0.1MES:NaOH pH 6.5, 10% PEG 4K, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.62 53.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.584 α = 90 b = 77.301 β = 99.75 c = 90.546 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 315r 2011-12-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97907 APS 19-ID
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 1.9 50 88.3 0.053 10 3.7 42672 42672 -3 23
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 1.9 1.92 62.9 0.2 2.2 1026
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 (All) 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 PDB ENTRY 1AD1 1.95 27.8 40678 40678 2060 90.43 0.1645 0.1645 0.1623 0.1728 0.2056 0.2102 RANDOM 33.391
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] 3.27 -0.8 -0.73 -2.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.343 r_dihedral_angle_4_deg 17.368 r_dihedral_angle_3_deg 12.58 r_dihedral_angle_1_deg 5.789 r_angle_refined_deg 1.615 r_angle_other_deg 0.835 r_chiral_restr 0.097 r_bond_refined_d 0.015 r_gen_planes_refined 0.007 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.343 r_dihedral_angle_4_deg 17.368 r_dihedral_angle_3_deg 12.58 r_dihedral_angle_1_deg 5.789 r_angle_refined_deg 1.615 r_angle_other_deg 0.835 r_chiral_restr 0.097 r_bond_refined_d 0.015 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3920 Nucleic Acid Atoms Solvent Atoms 269 Heterogen Atoms 28
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction SBC-Collect data collection HKL-3000 data reduction HKL-3000 data scaling HKL-3000 phasing SHELXD phasing SHELXE model building MLPHARE phasing DM phasing SOLVE phasing RESOLVE phasing ARP/wARP model building CCP4 phasing O model building Coot model building