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Structure of penicillin-binding protein A from M. tuberculosis: imipenem acyl-enzyme complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3LO7 PDB entry 3LO7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 292 20% PEG 3350, 0.2 M potassium nitrate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Crystal Properties Matthews coefficient Solvent content 2.27 45.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 122.8 α = 90 b = 122.8 β = 90 c = 101.1 γ = 120
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 2009-11-08 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) 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 2.1 46.1 98.1 0.075 37.4 11.3 49427 49427
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 2.1 2.18 89.3 0.638 1.7 7
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT PDB entry 3LO7 2.2 37.35 49400 41358 2149 99.08 0.21642 0.21421 0.25822 0.2439 RANDOM 44.516
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] 0.62 0.31 0.62 -0.93
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.081 r_dihedral_angle_4_deg 16.172 r_dihedral_angle_3_deg 16.112 r_dihedral_angle_1_deg 6.124 r_scangle_it 2.564 r_scbond_it 1.555 r_angle_refined_deg 1.337 r_mcangle_it 1.047 r_mcbond_it 0.619 r_nbtor_refined 0.296
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.081 r_dihedral_angle_4_deg 16.172 r_dihedral_angle_3_deg 16.112 r_dihedral_angle_1_deg 6.124 r_scangle_it 2.564 r_scbond_it 1.555 r_angle_refined_deg 1.337 r_mcangle_it 1.047 r_mcbond_it 0.619 r_nbtor_refined 0.296 r_symmetry_hbond_refined 0.251 r_nbd_refined 0.194 r_symmetry_vdw_refined 0.192 r_xyhbond_nbd_refined 0.125 r_chiral_restr 0.083 r_bond_refined_d 0.01 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6428 Nucleic Acid Atoms Solvent Atoms 57 Heterogen Atoms 40
Software Software Software Name Purpose SERGUI data collection REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling REFMAC phasing