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Complex between Penicillin-Binding Protein (PBP2) and MreC from Helicobacter pylori
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5LP4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 293 5%W/V PEG6000, 50MM CITRIC ACID PH 5, 9MM ZNCL2
Crystal Properties Matthews coefficient Solvent content 2.39 48.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 338.656 α = 90 b = 48.34 β = 113.02 c = 151.513 γ = 90
Symmetry Space Group C 1 2 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 MARMOSAIC 225 mm CCD 2009-04-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 0.87260 ESRF ID23-2
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 2.74 43.94 86.5 0.073 19.84 2.8 52464 3 45.79
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 2.74 2.9 83.1 0.41 3 2.8
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 5LP4 2.74 43.94 51156 1307 86.57 0.25771 0.25685 0.2667 0.29216 0.3047 RANDOM 60.029
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] -2.04 -2.5 6.19 -1.49
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.072 r_dihedral_angle_3_deg 14.372 r_dihedral_angle_4_deg 12.908 r_long_range_B_refined 9.759 r_long_range_B_other 9.759 r_dihedral_angle_1_deg 6.581 r_scangle_other 5.066 r_mcangle_it 5.035 r_mcangle_other 5.035 r_scbond_it 3.056
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.072 r_dihedral_angle_3_deg 14.372 r_dihedral_angle_4_deg 12.908 r_long_range_B_refined 9.759 r_long_range_B_other 9.759 r_dihedral_angle_1_deg 6.581 r_scangle_other 5.066 r_mcangle_it 5.035 r_mcangle_other 5.035 r_scbond_it 3.056 r_scbond_other 3.056 r_mcbond_it 3.053 r_mcbond_other 3.053 r_angle_refined_deg 1.28 r_angle_other_deg 0.854 r_chiral_restr 0.078 r_bond_refined_d 0.009 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 13312 Nucleic Acid Atoms Solvent Atoms 69 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing