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Structure of penicillin-binding protein 5 from E. coli: imipenem acyl-enzyme complex
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 7 294 100 MM TRIS PH 7.0, 8 % PEG 400, VAPOR DIFFUSION, SITTING DROP, temperature 294K
Crystal Properties Matthews coefficient Solvent content 2.53 51.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 109.78 α = 90 b = 50.35 β = 120.16 c = 84.29 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 2004-03-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.00 APS 22-ID
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 1.5 33 96.6 0.055 0.055 40.1 6.8 61886 61886 20.6
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.5 1.55 76.3 0.488 0.488 1.8 3.9 4880
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 PDB entry 1NZO 1.5 32.97 61823 61823 3123 96.7 0.189 0.189 0.188 0.212 0.2114 RANDOM 22.92
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] -0.16 -0.41 -0.56 0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.07 r_dihedral_angle_4_deg 18.226 r_dihedral_angle_3_deg 11.55 r_dihedral_angle_1_deg 5.506 r_rigid_bond_restr 5.095 r_scbond_it 4.443 r_scangle_it 3.948 r_sphericity_free 3.375 r_sphericity_bonded 3.37 r_mcangle_it 1.496
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.07 r_dihedral_angle_4_deg 18.226 r_dihedral_angle_3_deg 11.55 r_dihedral_angle_1_deg 5.506 r_rigid_bond_restr 5.095 r_scbond_it 4.443 r_scangle_it 3.948 r_sphericity_free 3.375 r_sphericity_bonded 3.37 r_mcangle_it 1.496 r_angle_refined_deg 1.225 r_mcbond_it 1.021 r_nbtor_refined 0.301 r_nbd_refined 0.193 r_symmetry_vdw_refined 0.115 r_xyhbond_nbd_refined 0.105 r_symmetry_hbond_refined 0.09 r_chiral_restr 0.079 r_bond_refined_d 0.009 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2740 Nucleic Acid Atoms Solvent Atoms 369 Heterogen Atoms 26
Software Software Software Name Purpose REFMAC refinement CNS refinement MAR345 data collection HKL-2000 data reduction SCALEPACK data scaling CNS phasing