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Penicillin-binding protein 2X (PBP 2X) acyl-enzyme complex (tebipenem) from Streptococcus pneumoniae
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2Z2L PDB ENTRY 2Z2L
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 10-25% PEG4000, 0.2M ammonium sulfate, 0.1M sodium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.76 55.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 107.305 α = 90 b = 172.063 β = 90 c = 88.805 γ = 90
Symmetry Space Group P 21 21 2
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 RIGAKU JUPITER 210 A fixed exit SI double crystal monochromator followed bystandard double crystal monochromator and RH-coated downward-deflection mirror with a typical glancing angle of 3.7MRAD 2004-12-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL32B2 1.0000 SPring-8 BL32B2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.8 29.69 99.7 0.07 14.4 5.6 41099 67.18
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.8 2.9 99.1 0.24 4.9 5.3
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-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2Z2L 2.8 29.69 39009 2059 99.66 0.22743 0.22497 0.27438 RANDOM 59.66
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] 1.22 -3.06 1.84
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.552 r_dihedral_angle_3_deg 15.713 r_dihedral_angle_4_deg 15.653 r_dihedral_angle_1_deg 5.499 r_scangle_it 1.128 r_angle_refined_deg 1.011 r_mcangle_it 0.772 r_scbond_it 0.659 r_mcbond_it 0.43 r_nbtor_refined 0.298
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.552 r_dihedral_angle_3_deg 15.713 r_dihedral_angle_4_deg 15.653 r_dihedral_angle_1_deg 5.499 r_scangle_it 1.128 r_angle_refined_deg 1.011 r_mcangle_it 0.772 r_scbond_it 0.659 r_mcbond_it 0.43 r_nbtor_refined 0.298 r_nbd_refined 0.193 r_symmetry_vdw_refined 0.161 r_xyhbond_nbd_refined 0.125 r_symmetry_hbond_refined 0.078 r_chiral_restr 0.068 r_bond_refined_d 0.007 r_gen_planes_refined 0.003 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9698 Nucleic Acid Atoms Solvent Atoms 33 Heterogen Atoms 55
Software Software Software Name Purpose REFMAC refinement BSS data collection CrystalClear data reduction CrystalClear data scaling