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1.8 Angstrom Resolution Crystal Structure of Dimerization and Transpeptidase domains (residues 39-608) of Penicillin-Binding Protein 1 from Staphylococcus aureus.
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.3 295 Protein: 10.8 mg/ml, 0.5M Sodium chloride, 0.01M Tris HCl (pH 8.3),
Screen: JCSG+ (A5), 0.2M Magnesium formate, 20% (w/v) PEG 3350.
Crystal Properties Matthews coefficient Solvent content 2.11 41.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 178.843 α = 90 b = 72.202 β = 103.18 c = 86.362 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 MARMOSAIC 300 mm CCD C(111) 2016-10-20 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) 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 1.8 30 99.7 0.088 0.088 26.8 5.4 98204 -3 30.3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.83 99.3 0.749 0.793 2.3 4.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 SAD THROUGHOUT 1.8 29.59 93238 4950 99.22 0.18088 0.17935 0.1931 0.20946 0.2231 RANDOM 43.7
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] 0.34 -1.07 -1.38 1.39
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.828 r_dihedral_angle_4_deg 10.696 r_dihedral_angle_3_deg 10.411 r_long_range_B_refined 5.186 r_long_range_B_other 5.028 r_dihedral_angle_1_deg 3.139 r_scangle_other 1.941 r_mcangle_it 1.739 r_mcangle_other 1.739 r_angle_refined_deg 1.365
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.828 r_dihedral_angle_4_deg 10.696 r_dihedral_angle_3_deg 10.411 r_long_range_B_refined 5.186 r_long_range_B_other 5.028 r_dihedral_angle_1_deg 3.139 r_scangle_other 1.941 r_mcangle_it 1.739 r_mcangle_other 1.739 r_angle_refined_deg 1.365 r_scbond_it 1.183 r_scbond_other 1.183 r_mcbond_it 1.066 r_mcbond_other 1.065 r_angle_other_deg 0.819 r_chiral_restr 0.085 r_gen_planes_refined 0.021 r_gen_planes_other 0.017 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 7959 Nucleic Acid Atoms Solvent Atoms 615 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling PHENIX phasing