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Crystal structure of Staphylococcus aureus metallopeptidase (Sapep/DapE) in the Mn2+ bound form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3KHX PDB ENTRY 3KHX, independent domains
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 Microbatch method under oil 6.8 293 0.2M Megnesium Acetate tetrahydrate, 0.1M Sodium Cacodylate pH 6.8, 22.0% Polyethylene glycol 8000, Microbatch method under oil, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.98 58.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 158.15 α = 90 b = 158.15 β = 90 c = 158.15 γ = 90
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE RIGAKU 2009-07-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE OTHER 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.9 50 100 0.108 0.115 14.2 7.9 14758 2 2 69.9
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.9 3.06 100 0.563 0.604 3.6 7.8 2141
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 PDB ENTRY 3KHX, independent domains 2.9 28.88 13998 745 99.99 0.20492 0.20212 0.2126 0.2626 0.2776 RANDOM 42.555
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.888 r_dihedral_angle_4_deg 20.69 r_dihedral_angle_3_deg 15.345 r_dihedral_angle_1_deg 4.845 r_scangle_it 1.232 r_angle_refined_deg 0.937 r_scbond_it 0.695 r_mcangle_it 0.577 r_mcbond_it 0.304 r_chiral_restr 0.065
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.888 r_dihedral_angle_4_deg 20.69 r_dihedral_angle_3_deg 15.345 r_dihedral_angle_1_deg 4.845 r_scangle_it 1.232 r_angle_refined_deg 0.937 r_scbond_it 0.695 r_mcangle_it 0.577 r_mcbond_it 0.304 r_chiral_restr 0.065 r_bond_refined_d 0.005 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3662 Nucleic Acid Atoms Solvent Atoms 26 Heterogen Atoms 7
Software Software Software Name Purpose MAR345dtb data collection PHASER phasing REFMAC refinement MOSFLM data reduction SCALA data scaling