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PENICILLIN-BINDING PROTEIN 1B (PBP-1B) IN COMPLEX WITH A MONOBACTAM (6)
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 3.29 62.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.655 α = 90 b = 148.242 β = 90 c = 98.83 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 1.88 44 97.6 0.066 0.998 8.39 3.9 56578 56.7
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 1.88 1.99 98 0.293 0.091 0.48 3.9
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 1.88 43.998 56519 2036 97.539 0.179 0.1779 0.1866 0.2217 0.2276 65.819
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] -2.123 1.148 0.974
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.397 r_dihedral_angle_3_deg 11.971 r_lrange_other 9.183 r_lrange_it 9.178 r_scangle_it 7.442 r_scangle_other 7.333 r_dihedral_angle_2_deg 7.013 r_dihedral_angle_1_deg 6.626 r_scbond_it 4.937 r_scbond_other 4.845
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.397 r_dihedral_angle_3_deg 11.971 r_lrange_other 9.183 r_lrange_it 9.178 r_scangle_it 7.442 r_scangle_other 7.333 r_dihedral_angle_2_deg 7.013 r_dihedral_angle_1_deg 6.626 r_scbond_it 4.937 r_scbond_other 4.845 r_mcangle_it 4.56 r_mcangle_other 4.56 r_mcbond_it 3.377 r_mcbond_other 3.376 r_angle_refined_deg 1.294 r_angle_other_deg 0.452 r_symmetry_nbd_refined 0.224 r_symmetry_xyhbond_nbd_refined 0.21 r_nbd_refined 0.209 r_symmetry_nbd_other 0.191 r_nbd_other 0.184 r_nbtor_refined 0.181 r_dihedral_angle_other_2_deg 0.152 r_xyhbond_nbd_refined 0.152 r_symmetry_nbtor_other 0.077 r_chiral_restr 0.066 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3488 Nucleic Acid Atoms Solvent Atoms 200 Heterogen Atoms 51
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing