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PENICILLIN-BINDING PROTEIN 1B (PBP-1B) in complex with 8Az lactone - Streptococcus pneumoniae R6
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2BG1 2BG1 WITHOUT RESIDUES 654 TO 660
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 63.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.934 α = 90 b = 149.773 β = 90 c = 98.872 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 PILATUS 2M 2021-02-01 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 1.744 42.251 97.1 0.1025 0.996 8.01 4.7 71666 38.906
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 1.744 1.85 91.6 1.972 0.248 0.65 4.4
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2BG1 WITHOUT RESIDUES 654 TO 660 1.744 42.251 71665 2192 97.736 0.181 0.1802 0.1905 0.2063 0.2178 52.285
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] -1.993 1.993
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.292 r_dihedral_angle_4_deg 17.911 r_dihedral_angle_3_deg 11.929 r_lrange_it 8.473 r_lrange_other 8.434 r_dihedral_angle_1_deg 7.272 r_scangle_it 5.899 r_scangle_other 5.898 r_scbond_it 4.202 r_scbond_other 4.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.292 r_dihedral_angle_4_deg 17.911 r_dihedral_angle_3_deg 11.929 r_lrange_it 8.473 r_lrange_other 8.434 r_dihedral_angle_1_deg 7.272 r_scangle_it 5.899 r_scangle_other 5.898 r_scbond_it 4.202 r_scbond_other 4.12 r_mcangle_other 3.117 r_mcangle_it 3.116 r_mcbond_it 2.529 r_mcbond_other 2.524 r_angle_other_deg 1.329 r_angle_refined_deg 1.242 r_symmetry_xyhbond_nbd_refined 0.22 r_nbd_refined 0.203 r_nbd_other 0.194 r_symmetry_nbd_other 0.188 r_nbtor_refined 0.166 r_xyhbond_nbd_refined 0.135 r_symmetry_nbd_refined 0.133 r_xyhbond_nbd_other 0.109 r_symmetry_nbtor_other 0.087 r_chiral_restr 0.06 r_gen_planes_refined 0.008 r_bond_refined_d 0.007 r_chiral_restr_other 0.001 r_gen_planes_other 0.001 r_bond_other_d
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3506 Nucleic Acid Atoms Solvent Atoms 383 Heterogen Atoms 55
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing