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Crystal structure of penicillin-binding protein 2 from Neisseria gonorrhoeae containing four mutations associated with penicillin resistance
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other Wild-type structure
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 294 2.2 M ammonium sulphate, 100 mM Tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal Properties Matthews coefficient Solvent content 3.84 67.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.6 α = 90 b = 137.2 β = 90 c = 229.8 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE MAR scanner 300 mm plate 2006-11-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 0.97934 APS 22-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.4 50 98 0.101 29.9 7.1 71399 71399 49.1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 2.49 83.5 0.52 2.7 4.3 5957
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT Wild-type structure 2.4 48.1 71366 71366 3558 97.7 0.219 0.219 0.217 0.253 0.2806 RANDOM 48.7
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] 0.51 -0.15 -0.36
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.69 r_dihedral_angle_4_deg 19.83 r_dihedral_angle_3_deg 18.09 r_dihedral_angle_1_deg 6.14 r_scangle_it 2.593 r_scbond_it 1.614 r_angle_refined_deg 1.39 r_mcangle_it 1.038 r_mcbond_it 0.604 r_nbtor_refined 0.296
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.69 r_dihedral_angle_4_deg 19.83 r_dihedral_angle_3_deg 18.09 r_dihedral_angle_1_deg 6.14 r_scangle_it 2.593 r_scbond_it 1.614 r_angle_refined_deg 1.39 r_mcangle_it 1.038 r_mcbond_it 0.604 r_nbtor_refined 0.296 r_nbd_refined 0.2 r_symmetry_vdw_refined 0.193 r_symmetry_hbond_refined 0.17 r_xyhbond_nbd_refined 0.137 r_chiral_restr 0.092 r_bond_refined_d 0.011 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6633 Nucleic Acid Atoms Solvent Atoms 79 Heterogen Atoms 87
Software Software Software Name Purpose MAR345 data collection REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling