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Crystal structure of penicillin-binding protein 3 from pseudomonas aeruginosa in complex with piperacillin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3OCL PDB ENTRY 3OCL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 293 2.5 M NaCl; 0.1 M imidazole, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.73 54.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.049 α = 71.26 b = 74.935 β = 86.04 c = 82.785 γ = 85.59
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 2M 2011-05-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.91730 Diamond I04-1
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 2.31 50 97.8 0.185 6 9.4 55461 -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 2.31 2.39 87.2 0.275 1.5 5.9 4929
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 PDB ENTRY 3OCL 2.31 47.1 52657 2804 97.81 0.2188 0.21714 0.2202 0.24965 0.2545 RANDOM 42.412
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] 1.07 0.93 0.85 1.26 2.32 -1.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.167 r_dihedral_angle_3_deg 14.911 r_dihedral_angle_4_deg 14.505 r_dihedral_angle_1_deg 5.685 r_angle_refined_deg 1.271 r_angle_other_deg 0.861 r_chiral_restr 0.066 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 r_bond_other_d 0.003
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.167 r_dihedral_angle_3_deg 14.911 r_dihedral_angle_4_deg 14.505 r_dihedral_angle_1_deg 5.685 r_angle_refined_deg 1.271 r_angle_other_deg 0.861 r_chiral_restr 0.066 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 r_bond_other_d 0.003 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7635 Nucleic Acid Atoms Solvent Atoms 276 Heterogen Atoms 97
Software Software Software Name Purpose MOLREP phasing REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling