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Crystal Structure of R350A mutant of Staphylococcus aureus metallopeptidase (Sapep/DapE) in the apo-form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3KHX PDB ENTRY 3KHX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 Microbatch method under oil 6.5 293 0.2M Ammonium Sulfate, 0.1M MES, 30.0% PEG Mono-methyl-ether 5000, pH 6.5, Microbatch method under oil, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.64 53.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.75 α = 90 b = 133.52 β = 95.59 c = 67.71 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 IMAGE PLATE MAR scanner 345 mm plate OSMIC MIRROR 2009-04-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU300 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 2.5 60.16 100 0.068 0.072 20.9 8.5 39597 2 2 58.5
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 2.5 2.64 100 0.414 0.442 4.9 8.4 5730
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 2.5 49.02 37576 1984 99.97 0.21077 0.20776 0.2149 0.2693 0.267 RANDOM 49.954
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] -0.4 -1.75 -2.31 2.37
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.307 r_dihedral_angle_4_deg 22.597 r_dihedral_angle_3_deg 18.953 r_dihedral_angle_1_deg 6.386 r_scangle_it 2.619 r_scbond_it 1.627 r_angle_refined_deg 1.35 r_mcangle_it 1.111 r_mcbond_it 0.588 r_chiral_restr 0.097
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.307 r_dihedral_angle_4_deg 22.597 r_dihedral_angle_3_deg 18.953 r_dihedral_angle_1_deg 6.386 r_scangle_it 2.619 r_scbond_it 1.627 r_angle_refined_deg 1.35 r_mcangle_it 1.111 r_mcbond_it 0.588 r_chiral_restr 0.097 r_bond_refined_d 0.011 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6767 Nucleic Acid Atoms Solvent Atoms 113 Heterogen Atoms
Software Software Software Name Purpose MAR345dtb data collection PHASER phasing REFMAC refinement MOSFLM data reduction SCALA data scaling