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Crystal Structure of the Peptidoglycan Binding Domain of the Outer Membrane Protein (OmpA) from Klebsiella pneumoniae with bound D-alanine
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 292 Protein: 9.4 mg/ml, 0.15M Sodium chloride, 0.01M Tris pH 8.3;
Screen: PEG's II (C4), 0.2M Magnesium chloride, 0.1M MES pH 6.5, 10% (w/v) PEG4000;
Cryo: 0.2M Magnesium chloride, 0.1M MES pH 6.5, 25% (w/v) PEG4000
Crystal Properties Matthews coefficient Solvent content 2.37 48.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.887 α = 90 b = 41.887 β = 90 c = 267.934 γ = 120
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 MARMOSAIC 300 mm CCD Be 2021-02-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 1.88 30 99.9 0.073 0.073 0.076 0.023 0.988 31.5 11.4 21507 -3 17.3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.88 1.91 100 1.358 1.358 0.439 0.626 1.8 10.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION SAD THROUGHOUT 1.88 28.16 19054 932 93.17 0.2022 0.2009 0.2284 0.2237 RANDOM 22.826
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] -0.01 -0.01 0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 21.663 r_dihedral_angle_4_deg 13.303 r_dihedral_angle_3_deg 10.148 r_dihedral_angle_1_deg 3.497 r_angle_refined_deg 1.442 r_angle_other_deg 0.361 r_chiral_restr 0.059 r_gen_planes_refined 0.054 r_gen_planes_other 0.048 r_bond_refined_d 0.006
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 21.663 r_dihedral_angle_4_deg 13.303 r_dihedral_angle_3_deg 10.148 r_dihedral_angle_1_deg 3.497 r_angle_refined_deg 1.442 r_angle_other_deg 0.361 r_chiral_restr 0.059 r_gen_planes_refined 0.054 r_gen_planes_other 0.048 r_bond_refined_d 0.006 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1848 Nucleic Acid Atoms Solvent Atoms 178 Heterogen Atoms 14
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-3000 data reduction HKL-3000 data scaling HKL-3000 phasing