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Penicillin-binding protein 1A (PBP 1A) acyl-enzyme complex (tebipenem) from Streptococcus pneumoniae
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2C6W PDB ENTRY 2C6W
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.8 293 0.004-0.006M ZINC SULFATE, 0.05M MES, pH6.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.77 55.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 185.755 α = 90 b = 50.277 β = 90 c = 109.535 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 ADSC QUANTUM 315 Rotated-inclined double-crystal monochromator, rhodium-coated horizontal mirror 2006-07-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1.0000 SPring-8 BL41XU
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 2.7 29.88 100 0.123 7.2 4.5 29074 56.87
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) 2.7 2.8 99.6 0.364 2.7 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 (Observed) R-Work (Depositor) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2C6W 2.7 29.88 27562 1473 99.86 0.23019 0.22796 0.27099 RANDOM 41.98
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] -0.46 0.13 0.33
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.243 r_dihedral_angle_4_deg 18.4 r_dihedral_angle_3_deg 16.327 r_dihedral_angle_1_deg 5.519 r_scangle_it 1.043 r_angle_refined_deg 1.024 r_mcangle_it 0.72 r_scbond_it 0.602 r_mcbond_it 0.394 r_nbtor_refined 0.302
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.243 r_dihedral_angle_4_deg 18.4 r_dihedral_angle_3_deg 16.327 r_dihedral_angle_1_deg 5.519 r_scangle_it 1.043 r_angle_refined_deg 1.024 r_mcangle_it 0.72 r_scbond_it 0.602 r_mcbond_it 0.394 r_nbtor_refined 0.302 r_symmetry_vdw_refined 0.22 r_nbd_refined 0.194 r_symmetry_hbond_refined 0.146 r_xyhbond_nbd_refined 0.136 r_metal_ion_refined 0.105 r_symmetry_metal_ion_refined 0.081 r_chiral_restr 0.073 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_other r_symmetry_vdw_other r_symmetry_hbond_other 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 6300 Nucleic Acid Atoms Solvent Atoms 40 Heterogen Atoms 58
Software Software Software Name Purpose REFMAC refinement BSS data collection CrystalClear data reduction CrystalClear data scaling MOLREP phasing