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PENICILLIN-BINDING PROTEIN 1B (PBP-1B) in complex with lactone 5Az - 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 3.3 62.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.025 α = 90 b = 149.061 β = 90 c = 99.226 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 1.568 48.02 99.3 0.067 0.997 10.62 4.7 98508 34.821
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 1.568 1.66 99.4 1.221 0.447 1.09 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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2BG1 WITHOUT RESIDUES 654 TO 660 1.57 48.013 98507 2458 99.343 0.155 0.1538 0.1814 0.2132 41.839
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] 0.293 0.091 -0.384
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.69 r_dihedral_angle_4_deg 13.004 r_dihedral_angle_3_deg 12.022 r_lrange_it 7.954 r_lrange_other 7.801 r_dihedral_angle_1_deg 7.105 r_scangle_it 5.846 r_scangle_other 5.845 r_scbond_it 4.087 r_scbond_other 4.086
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.69 r_dihedral_angle_4_deg 13.004 r_dihedral_angle_3_deg 12.022 r_lrange_it 7.954 r_lrange_other 7.801 r_dihedral_angle_1_deg 7.105 r_scangle_it 5.846 r_scangle_other 5.845 r_scbond_it 4.087 r_scbond_other 4.086 r_mcangle_it 2.628 r_mcangle_other 2.628 r_mcbond_it 2.126 r_mcbond_other 2.126 r_angle_other_deg 1.419 r_angle_refined_deg 1.245 r_symmetry_xyhbond_nbd_refined 0.288 r_nbd_refined 0.209 r_nbd_other 0.2 r_symmetry_nbd_other 0.192 r_symmetry_nbd_refined 0.19 r_nbtor_refined 0.172 r_xyhbond_nbd_refined 0.154 r_symmetry_nbtor_other 0.088 r_chiral_restr 0.073 r_xyhbond_nbd_other 0.033 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_chiral_restr_other r_gen_planes_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3506 Nucleic Acid Atoms Solvent Atoms 589 Heterogen Atoms 51
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing