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PENICILLIN-BINDING PROTEIN 1B (PBP-1B) in complex with lactone 6Az - 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 3.29 62.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.306 α = 90 b = 149.053 β = 90 c = 98.835 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 2021-06-10 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 1.535 44.16 98.4 0.131 0.985 5.93 4.8 105235 35.582
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 1.535 1.63 93.1 1.663 0.325 0.74 4.6
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 1.55 44.155 102341 2034 99.432 0.166 0.1654 0.1719 0.1897 0.1982 42.832
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] 0.906 -0.331 -0.575
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.412 r_dihedral_angle_4_deg 12.095 r_dihedral_angle_3_deg 11.366 r_lrange_it 8.436 r_lrange_other 8.37 r_dihedral_angle_1_deg 6.42 r_scangle_it 5.187 r_scangle_other 5.186 r_scbond_it 3.499 r_scbond_other 3.498
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.412 r_dihedral_angle_4_deg 12.095 r_dihedral_angle_3_deg 11.366 r_lrange_it 8.436 r_lrange_other 8.37 r_dihedral_angle_1_deg 6.42 r_scangle_it 5.187 r_scangle_other 5.186 r_scbond_it 3.499 r_scbond_other 3.498 r_mcangle_it 2.451 r_mcangle_other 2.451 r_mcbond_it 1.911 r_mcbond_other 1.911 r_angle_other_deg 1.402 r_angle_refined_deg 1.223 r_xyhbond_nbd_other 0.49 r_symmetry_xyhbond_nbd_refined 0.39 r_symmetry_nbd_refined 0.326 r_nbd_other 0.221 r_nbd_refined 0.21 r_symmetry_nbd_other 0.193 r_nbtor_refined 0.17 r_xyhbond_nbd_refined 0.146 r_symmetry_nbtor_other 0.089 r_chiral_restr 0.062 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d r_gen_planes_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3506 Nucleic Acid Atoms Solvent Atoms 549 Heterogen Atoms 51
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing