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Crystal structure of E. coli penicillin-binding protein 5 in complex with a peptide-mimetic cephalosporin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1NZO PDB entry 1NZO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 294 100mM Tris pH 8.0, 8% PEG 400, VAPOR DIFFUSION, SITTING DROP, temperature 294K
Crystal Properties Matthews coefficient Solvent content 2.54 51.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 109.5 α = 90 b = 50.5 β = 121.1 c = 85.4 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 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 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 1.6 41 97.3 0.074 25.7 3.5 51428 51428
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 1.6 1.66 82.7 0.414 1.8 2.5
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 FOURIER SYNTHESIS THROUGHOUT PDB entry 1NZO 1.6 40.82 51415 48813 2602 97.15 0.19328 0.19215 0.197 0.21473 0.2213 RANDOM 16.458
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] -0.7 -0.68 0.35 -0.35
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.319 r_dihedral_angle_4_deg 13.97 r_dihedral_angle_3_deg 12.099 r_dihedral_angle_1_deg 5.675 r_sphericity_free 4.778 r_scangle_it 3.276 r_sphericity_bonded 2.323 r_scbond_it 2.32 r_mcangle_it 1.646 r_rigid_bond_restr 1.546
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.319 r_dihedral_angle_4_deg 13.97 r_dihedral_angle_3_deg 12.099 r_dihedral_angle_1_deg 5.675 r_sphericity_free 4.778 r_scangle_it 3.276 r_sphericity_bonded 2.323 r_scbond_it 2.32 r_mcangle_it 1.646 r_rigid_bond_restr 1.546 r_angle_refined_deg 1.295 r_mcbond_it 1.137 r_angle_other_deg 0.872 r_mcbond_other 0.405 r_nbd_refined 0.201 r_symmetry_vdw_other 0.194 r_nbd_other 0.191 r_nbtor_refined 0.177 r_xyhbond_nbd_refined 0.148 r_symmetry_hbond_refined 0.137 r_symmetry_vdw_refined 0.13 r_nbtor_other 0.086 r_chiral_restr 0.078 r_bond_refined_d 0.011 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2713 Nucleic Acid Atoms Solvent Atoms 260 Heterogen Atoms 37
Software Software Software Name Purpose REFMAC refinement SERGUI data collection HKL-2000 data reduction SCALEPACK data scaling