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PENICILLIN-BINDING PROTEIN 2B (PBP-2B) FROM STREPTOCOCCUS PNEUMONIAE (STRAIN 5204)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8 100 MM BIS-TRIS-HCL PH 5.5, 300 MM NACL, 5 MM ZN ACETATE, 30% W/V POLYETHYLENE GLYCOL MME 550
Crystal Properties Matthews coefficient Solvent content 2.3 55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 128.788 α = 90 b = 128.788 β = 90 c = 123.139 γ = 120
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 2007-06-10 M SINGLE WAVELENGTH 2 1 x-ray CCD ADSC CCD M
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-3 ESRF ID14-3 2 SYNCHROTRON ESRF BEAMLINE BM30A 1.282740, 1.283334, 1.279625 ESRF BM30A
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 2.18 44.5 91 0.07 17.34 4.4 108466 3 46.42
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 2.18 2.31 70.1 0.6 2.97 4
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 MAD THROUGHOUT NONE 2.18 44.5 110872 5889 100 0.213 0.211 0.2194 0.261 0.2686 RANDOM 49.53
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] 0.53 0.26 0.53 -0.79
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.74 r_dihedral_angle_4_deg 20.839 r_dihedral_angle_3_deg 16.945 r_dihedral_angle_1_deg 6.184 r_scangle_it 5.992 r_scbond_it 4.099 r_mcangle_it 2.533 r_mcbond_it 1.542 r_angle_refined_deg 1.342 r_chiral_restr 0.109
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.74 r_dihedral_angle_4_deg 20.839 r_dihedral_angle_3_deg 16.945 r_dihedral_angle_1_deg 6.184 r_scangle_it 5.992 r_scbond_it 4.099 r_mcangle_it 2.533 r_mcbond_it 1.542 r_angle_refined_deg 1.342 r_chiral_restr 0.109 r_bond_refined_d 0.007 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 13812 Nucleic Acid Atoms Solvent Atoms 570 Heterogen Atoms 9
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling autoSHARP phasing