☰ Navigation Tabs
Structure of R504C mutant of Pseudomonas aeruginosa Penicillin-Binding Protein 3 (PBP3) in complex with piperacillin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3OC2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 25% (w/v) polyethylene glycol 3 350, 0.1 M Bis-Tris propane pH 7.8 and 1% (w/v) protamine sulphate
Crystal Properties Matthews coefficient Solvent content 2.15 42.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.44 α = 90 b = 82.64 β = 90 c = 88.76 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 PIXEL DECTRIS PILATUS 6M-F 2016-09-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.98 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.72 54.23 100 13.8 11.5 54141
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.72 1.75 0.5
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 3OC2 1.72 54.2 51309 2761 99.88 0.21061 0.20846 0.2179 0.25055 0.2615 RANDOM 33.939
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] 2.95 -0.93 -2.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.086 r_dihedral_angle_4_deg 17.131 r_dihedral_angle_3_deg 15.608 r_long_range_B_refined 7.339 r_long_range_B_other 7.336 r_dihedral_angle_1_deg 7.087 r_scangle_other 5.594 r_mcangle_it 4.18 r_mcangle_other 4.18 r_scbond_it 3.8
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.086 r_dihedral_angle_4_deg 17.131 r_dihedral_angle_3_deg 15.608 r_long_range_B_refined 7.339 r_long_range_B_other 7.336 r_dihedral_angle_1_deg 7.087 r_scangle_other 5.594 r_mcangle_it 4.18 r_mcangle_other 4.18 r_scbond_it 3.8 r_scbond_other 3.799 r_mcbond_it 2.908 r_mcbond_other 2.901 r_angle_refined_deg 2.002 r_angle_other_deg 1.139 r_chiral_restr 0.162 r_bond_refined_d 0.02 r_gen_planes_refined 0.011 r_bond_other_d 0.002 r_gen_planes_other 0.002 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3975 Nucleic Acid Atoms Solvent Atoms 118 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling MOLREP phasing