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1.67 Angstrom Resolution Crystal Structure of Murein-DD-endopeptidase from Yersinia enterocolitica.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6AZI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 292 Protein: 7.5 mg/ml, 0.01M Tris HCl (pH 8.3);
Screen: PEG's II (D1), 0.1M Sodium acetate, 0.1M HEPES (pH 7.5), 22% (w/v) PEG 4000.
Crystal Properties Matthews coefficient Solvent content 1.75 29.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.201 α = 90 b = 37.858 β = 115.75 c = 59.577 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 100 CCD MARMOSAIC 300 mm CCD C(111) 2018-10-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.97856 APS 21-ID-G
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) 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 1.67 30 99.9 0.072 0.072 0.083 0.039 22.4 4.3 26136 -3 27.6
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.67 1.7 99.9 0.709 0.709 0.814 0.395 0.766 2 4.1
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 6AZI 1.67 29.83 24714 1283 99.83 0.17091 0.16922 0.182 0.20354 0.2168 RANDOM 35.818
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] 0.86 -2.31 0.06 0.89
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 23.024 r_dihedral_angle_4_deg 13.583 r_dihedral_angle_3_deg 9.521 r_long_range_B_refined 5.536 r_long_range_B_other 5.471 r_dihedral_angle_1_deg 3.001 r_scangle_other 2.727 r_mcangle_it 1.94 r_mcangle_other 1.94 r_scbond_it 1.719
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 23.024 r_dihedral_angle_4_deg 13.583 r_dihedral_angle_3_deg 9.521 r_long_range_B_refined 5.536 r_long_range_B_other 5.471 r_dihedral_angle_1_deg 3.001 r_scangle_other 2.727 r_mcangle_it 1.94 r_mcangle_other 1.94 r_scbond_it 1.719 r_scbond_other 1.717 r_angle_refined_deg 1.445 r_mcbond_it 1.271 r_mcbond_other 1.265 r_angle_other_deg 0.409 r_chiral_restr 0.062 r_gen_planes_refined 0.051 r_gen_planes_other 0.047 r_bond_refined_d 0.006 r_bond_other_d 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 2062 Nucleic Acid Atoms Solvent Atoms 178 Heterogen Atoms 9
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling MoRDa phasing