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Penicillin-Binding Protein (PBP2) from Helicobacter pylori
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3PBN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 293 1.4M (NH4)2SO4, 50MM HEPES-NA PH 7
Crystal Properties Matthews coefficient Solvent content 2.17 43.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.397 α = 90 b = 140.965 β = 101.67 c = 81.297 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 273 CCD ADSC QUANTUM 315r 2013-07-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM30A 0.979526 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 3.03 45.39 90.8 0.12 12.15 3 27837 3 37.46
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) 1 3.03 3.21 84.5 0.43 3.01 2.9
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 3PBN 3.03 45.39 25070 2766 91.03 0.25467 0.25097 0.2521 0.28766 0.2852 RANDOM 51.474
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] 2.33 -0.46 -4.12 1.83
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.637 r_dihedral_angle_4_deg 16.581 r_dihedral_angle_3_deg 15.326 r_dihedral_angle_1_deg 6.492 r_long_range_B_refined 5.99 r_long_range_B_other 5.99 r_mcangle_it 3.62 r_mcangle_other 3.62 r_scangle_other 3.277 r_mcbond_it 2.081
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.637 r_dihedral_angle_4_deg 16.581 r_dihedral_angle_3_deg 15.326 r_dihedral_angle_1_deg 6.492 r_long_range_B_refined 5.99 r_long_range_B_other 5.99 r_mcangle_it 3.62 r_mcangle_other 3.62 r_scangle_other 3.277 r_mcbond_it 2.081 r_mcbond_other 2.081 r_scbond_it 1.847 r_scbond_other 1.84 r_angle_refined_deg 1.268 r_angle_other_deg 0.819 r_chiral_restr 0.07 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 r_bond_other_d 0.003 r_gen_planes_other 0.002 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8332 Nucleic Acid Atoms Solvent Atoms 24 Heterogen Atoms 15
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling BALBES phasing