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Cefditoren-Acylated Penicillin-Binding Protein 2X (PBP2X) from Streptococcus pneumoniae
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2Z2L
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 10-25% PEG4000, 0.2M ammonium sulfate, 0.1M sodium acetate, VAPOR DIFFUSION, HANGING DROP
Crystal Properties Matthews coefficient Solvent content 2.77 55.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 107.735 α = 90 b = 171.205 β = 90 c = 89.15 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 2005-11-11 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 2.6 30 89.9 0.054 16.7 4.3 46229 60.179
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) 2.6 2.69 90.5 0.215 5.5 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-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2Z2L 2.6 29.42 43896 2288 89.8 0.22279 0.22052 0.26711 RANDOM 46.402
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] 0.41 -0.46 0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.726 r_dihedral_angle_3_deg 14.481 r_dihedral_angle_4_deg 14.432 r_dihedral_angle_1_deg 5.216 r_scangle_it 1.144 r_angle_refined_deg 0.996 r_mcangle_it 0.733 r_scbond_it 0.679 r_mcbond_it 0.409 r_nbtor_refined 0.295
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.726 r_dihedral_angle_3_deg 14.481 r_dihedral_angle_4_deg 14.432 r_dihedral_angle_1_deg 5.216 r_scangle_it 1.144 r_angle_refined_deg 0.996 r_mcangle_it 0.733 r_scbond_it 0.679 r_mcbond_it 0.409 r_nbtor_refined 0.295 r_nbd_refined 0.18 r_symmetry_vdw_refined 0.16 r_xyhbond_nbd_refined 0.133 r_symmetry_hbond_refined 0.107 r_chiral_restr 0.067 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 9453 Nucleic Acid Atoms Solvent Atoms 93 Heterogen Atoms 71
Software Software Software Name Purpose REFMAC refinement BSS data collection CrystalClear data reduction CrystalClear data scaling MOLREP phasing