☰ Navigation Tabs
PENICILLIN-BINDING PROTEIN 2B (PBP-2B) FROM STREPTOCOCCUS PNEUMONIAE (STRAIN R6)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2WAD PDB ENTRY 2WAD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8 1.4M (NH4)2SO4, pH 8
Crystal Properties Matthews coefficient Solvent content 3.8 67.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 193.897 α = 90 b = 51.593 β = 112.38 c = 121.44 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC CCD 1999-07-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 ESRF ID14-4
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) 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 3.29 47.25 82.5 0.1 11.2 3.4 14291 3 69.16
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.29 3.49 54.9 0.44 2.82 3
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2WAD 3.29 47.25 15012 770 100 0.24 0.237 0.2346 0.287 0.286 RANDOM 91.21
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] -2.67 2.57 -0.08 4.71
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.541 r_dihedral_angle_3_deg 19.993 r_dihedral_angle_4_deg 18.503 r_dihedral_angle_1_deg 7.344 r_scangle_it 4.636 r_scbond_it 2.57 r_mcangle_it 1.781 r_angle_refined_deg 1.287 r_mcbond_it 0.906 r_chiral_restr 0.093
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.541 r_dihedral_angle_3_deg 19.993 r_dihedral_angle_4_deg 18.503 r_dihedral_angle_1_deg 7.344 r_scangle_it 4.636 r_scbond_it 2.57 r_mcangle_it 1.781 r_angle_refined_deg 1.287 r_mcbond_it 0.906 r_chiral_restr 0.093 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4701 Nucleic Acid Atoms Solvent Atoms 11 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing