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PENICILLIN-BINDING PROTEIN 1B (PBP-1B) IN COMPLEX WITH A MONOBACTAM (10)
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 3.33 63.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.483 α = 90 b = 149.563 β = 90 c = 99.467 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 1.74 44.3 96.7 0.058 0.999 9.88 4.2 71443 48.21
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 1.74 1.84 97.7 1.8 0.206 0.53 4.1
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 1.74 44.291 71392 2185 96.669 0.176 0.1754 0.1854 0.2015 0.2099 51.83
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] 0.305 0.42 -0.725
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.225 r_dihedral_angle_3_deg 11.844 r_dihedral_angle_2_deg 11.459 r_lrange_it 9.167 r_lrange_other 9.115 r_scangle_it 6.86 r_scangle_other 6.859 r_dihedral_angle_other_2_deg 6.791 r_dihedral_angle_1_deg 6.696 r_scbond_it 4.49
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.225 r_dihedral_angle_3_deg 11.844 r_dihedral_angle_2_deg 11.459 r_lrange_it 9.167 r_lrange_other 9.115 r_scangle_it 6.86 r_scangle_other 6.859 r_dihedral_angle_other_2_deg 6.791 r_dihedral_angle_1_deg 6.696 r_scbond_it 4.49 r_scbond_other 4.489 r_mcangle_other 3.496 r_mcangle_it 3.494 r_mcbond_it 2.691 r_mcbond_other 2.687 r_angle_refined_deg 1.298 r_angle_other_deg 0.461 r_nbd_refined 0.208 r_symmetry_xyhbond_nbd_refined 0.187 r_symmetry_nbd_other 0.183 r_nbtor_refined 0.18 r_symmetry_nbd_refined 0.176 r_nbd_other 0.164 r_xyhbond_nbd_refined 0.133 r_symmetry_nbtor_other 0.076 r_chiral_restr 0.071 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 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 329 Heterogen Atoms 51
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing