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PENICILLIN-BINDING PROTEIN 1B (PBP-1B) IN COMPLEX WITH A MONOBACTAM (15)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2BG1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.2 293 50MM HEPES PH 7.2, 3M NACL, 0.6-0.9M AMMONIUM SULFATE
Crystal Properties Matthews coefficient Solvent content 3.28 62.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.404 α = 90 b = 148.533 β = 90 c = 98.61 γ = 90
Symmetry Space Group C 2 2 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 PILATUS3 6M 2024-04-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-1 0.965459 ESRF MASSIF-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) CC (Half) 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 1.81 44.05 95.8 0.058 0.998 11.31 3.8 61904 49.02
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.81 1.92 96.2 0.139 0.491 1.13 3.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.811 44.042 61903 2044 95.908 0.161 0.1601 0.17 0.1809 0.1869 51.291
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] -0.628 0.801 -0.173
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.426 r_dihedral_angle_3_deg 11.302 r_lrange_it 8.736 r_lrange_other 8.699 r_dihedral_angle_1_deg 6.609 r_dihedral_angle_2_deg 6.59 r_scangle_it 6.313 r_scangle_other 6.311 r_scbond_it 4.298 r_scbond_other 4.297
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.426 r_dihedral_angle_3_deg 11.302 r_lrange_it 8.736 r_lrange_other 8.699 r_dihedral_angle_1_deg 6.609 r_dihedral_angle_2_deg 6.59 r_scangle_it 6.313 r_scangle_other 6.311 r_scbond_it 4.298 r_scbond_other 4.297 r_mcangle_other 3.429 r_mcangle_it 3.425 r_dihedral_angle_other_2_deg 2.932 r_mcbond_it 2.589 r_mcbond_other 2.576 r_angle_refined_deg 1.289 r_angle_other_deg 0.46 r_symmetry_xyhbond_nbd_refined 0.258 r_nbd_refined 0.208 r_symmetry_nbd_other 0.184 r_nbtor_refined 0.181 r_nbd_other 0.163 r_symmetry_nbd_refined 0.162 r_xyhbond_nbd_refined 0.147 r_symmetry_nbtor_other 0.075 r_chiral_restr 0.072 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3515 Nucleic Acid Atoms Solvent Atoms 356 Heterogen Atoms 49
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing