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Catalytic domain of the antimicrobial peptidase lysostaphin from Staphylococcus simulans crystallized in the presence of phosphate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4LXC PDB ENTRY 4LXC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 0.05 M potassium dihydrogen phosphate, 20 % w/v PEG 8000 and 6 mM glycine hydroxamate supplemented with 10% (v/v) glycerol for cryocooling. Crystal was soaked for 5 min with 25 mM iodo-GGSGG pentapeptide dissolved in the buffer used for cryocooling, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.03 39.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 34.279 α = 90 b = 106.78 β = 97.42 c = 34.331 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 PIXEL DECTRIS PILATUS 6M 2013-11-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 BESSY 14.1
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 1.26 35.6 98.3 0.072 13.23 5.77 64943
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.26 1.33 90.9 0.412 2.49 4.47
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT PDB ENTRY 4LXC 1.26 34.04 1.42 64902 64902 2039 98.3 0.133 0.13 0.1337 0.175 0.1724
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] -1.9557 1.0607 3.6445 -1.6888
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 12.654 f_angle_d 1.153 f_chiral_restr 0.074 f_bond_d 0.01 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2086 Nucleic Acid Atoms Solvent Atoms 219 Heterogen Atoms 24
Software Software Software Name Purpose MOLREP phasing PHENIX refinement XDS data reduction XDS data scaling