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Crystal structure of penicillin-binding protein 3 from Pseudomonas aeruginosa in complex with carbenicillin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3EQU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 294 20%(w/v) polyethylene glycol 3350, 0.2M di-sodium tartrate, 0.5mM carbenicillin, VAPOR DIFFUSION, SITTING DROP, temperature 294K
Crystal Properties Matthews coefficient Solvent content 2.13 42.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.475 α = 90 b = 83.435 β = 90 c = 89.845 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 CCD MARMOSAIC 225 mm CCD 2009-09-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 0.8726 ESRF ID23-2
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 2.3 30 99.8 0.209 7.8 5.9 24040 -1.5
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 2.3 2.38 99.9 0.872 1.5 5.6 2367
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 MOLECULAR REPLACEMENT THROUGHOUT 3EQU 2.3 28.19 22550 1233 99.84 0.20388 0.20151 0.203 0.24794 0.2516 RANDOM 26.268
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] 0.28 1.92 -2.2
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.402 r_dihedral_angle_3_deg 15.598 r_dihedral_angle_4_deg 14.335 r_dihedral_angle_1_deg 5.35 r_angle_refined_deg 1.127 r_angle_other_deg 0.852 r_chiral_restr 0.065 r_bond_refined_d 0.007 r_gen_planes_refined 0.004 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.402 r_dihedral_angle_3_deg 15.598 r_dihedral_angle_4_deg 14.335 r_dihedral_angle_1_deg 5.35 r_angle_refined_deg 1.127 r_angle_other_deg 0.852 r_chiral_restr 0.065 r_bond_refined_d 0.007 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 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_mcbond_it r_mcbond_other r_mcangle_it r_scbond_it 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 3801 Nucleic Acid Atoms Solvent Atoms 143 Heterogen Atoms 33
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling REFMAC phasing