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PENICILLIN-BINDING PROTEIN 1B (PBP-1B) in complex with lactone 7Az - 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 63.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.608 α = 90 b = 148.936 β = 90 c = 99.704 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 1.631 44.16 96.8 0.069 0.998 10.16 4.4 86692 36.378
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 1.631 1.73 93.6 1.628 0.275 0.74
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 1.631 44.156 86692 2169 96.985 0.169 0.1684 0.176 0.1873 0.1918 46.072
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] -0.777 0.449 0.328
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.167 r_dihedral_angle_4_deg 16.416 r_dihedral_angle_3_deg 12.357 r_lrange_it 8.156 r_lrange_other 8.089 r_dihedral_angle_1_deg 7.345 r_scangle_it 5.24 r_scangle_other 5.239 r_scbond_it 3.554 r_scbond_other 3.553
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.167 r_dihedral_angle_4_deg 16.416 r_dihedral_angle_3_deg 12.357 r_lrange_it 8.156 r_lrange_other 8.089 r_dihedral_angle_1_deg 7.345 r_scangle_it 5.24 r_scangle_other 5.239 r_scbond_it 3.554 r_scbond_other 3.553 r_mcangle_it 2.713 r_mcangle_other 2.712 r_mcbond_it 2.088 r_mcbond_other 2.088 r_angle_refined_deg 1.209 r_angle_other_deg 1.038 r_symmetry_xyhbond_nbd_refined 0.224 r_nbd_refined 0.206 r_nbd_other 0.194 r_symmetry_nbd_other 0.18 r_nbtor_refined 0.172 r_xyhbond_nbd_other 0.153 r_xyhbond_nbd_refined 0.145 r_symmetry_nbd_refined 0.108 r_symmetry_nbtor_other 0.09 r_chiral_restr 0.06 r_gen_planes_refined 0.029 r_gen_planes_other 0.025 r_bond_refined_d 0.007 r_symmetry_xyhbond_nbd_other 0.006 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3506 Nucleic Acid Atoms Solvent Atoms 495 Heterogen Atoms 55
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing