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PENICILLIN-BINDING PROTEIN 1B (PBP-1B) 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 3.32 61.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 95.681 α = 90 b = 147.016 β = 90 c = 98.709 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 1.467 43.06 99.5 0.078 0.998 11.77 5.2 117495 30.38
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 1.467 1.55 99.3 1.973 0.298 0.87 4.9
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 1.467 43.051 117495 2358 99.107 0.19 0.1894 0.1798 0.1995 0.1956 46.129
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] 0.483 -0.109 -0.373
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.903 r_dihedral_angle_4_deg 20.246 r_dihedral_angle_3_deg 13.052 r_lrange_it 9.103 r_lrange_other 8.913 r_dihedral_angle_1_deg 7.757 r_scangle_it 5.462 r_scangle_other 5.461 r_scbond_it 3.757 r_scbond_other 3.756
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.903 r_dihedral_angle_4_deg 20.246 r_dihedral_angle_3_deg 13.052 r_lrange_it 9.103 r_lrange_other 8.913 r_dihedral_angle_1_deg 7.757 r_scangle_it 5.462 r_scangle_other 5.461 r_scbond_it 3.757 r_scbond_other 3.756 r_mcangle_it 3.102 r_mcangle_other 3.101 r_mcbond_it 2.473 r_mcbond_other 2.461 r_angle_refined_deg 1.234 r_angle_other_deg 0.988 r_nbd_refined 0.217 r_symmetry_nbd_other 0.191 r_symmetry_xyhbond_nbd_refined 0.186 r_nbtor_refined 0.178 r_xyhbond_nbd_refined 0.168 r_nbd_other 0.137 r_symmetry_nbd_refined 0.124 r_symmetry_nbtor_other 0.089 r_chiral_restr 0.062 r_gen_planes_refined 0.034 r_gen_planes_other 0.029 r_bond_refined_d 0.009 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3615 Nucleic Acid Atoms Solvent Atoms 677 Heterogen Atoms 26
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing