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Catalytic domain of the antimicrobial peptidase lysostaphin from Staphylococcus simulans crystallized in the absence of phosphate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4QP5 pdb entry 4QP5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 6 mM pentapeptide GGSGG, 0.1 M Tris (base), Bicine pH 8.5, 0.1 M amino acids (L-Na-glutamate, alanine (racemic), glycine; lysine-HCl (racemic); serine (racemic)), 30% v/v precipitant (ethylene glycol, PEG 8000)., VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.04 39.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 34.289 α = 90 b = 107.318 β = 97.63 c = 34.307 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 2013-10-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.2 0.9184 BESSY 14.2
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 1.78 35 99.1 0.167 7.52 2.74 23389 23389
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 1.78 1.89 98.8 0.586 2.1 2.73 3748
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT pdb entry 4QP5 1.78 33.99 23387 23387 707 99.19 0.21133 0.21025 0.2157 0.24432 0.2473 THIN RESOLUTION SHELLS 12.819
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] -1.36 0.02 1.61 -0.24
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.937 r_dihedral_angle_4_deg 22.563 r_dihedral_angle_3_deg 13.202 r_dihedral_angle_1_deg 6.904 r_scangle_it 3.932 r_scbond_it 2.679 r_angle_refined_deg 1.754 r_mcangle_it 1.684 r_angle_other_deg 1.388 r_mcbond_it 1.043
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.937 r_dihedral_angle_4_deg 22.563 r_dihedral_angle_3_deg 13.202 r_dihedral_angle_1_deg 6.904 r_scangle_it 3.932 r_scbond_it 2.679 r_angle_refined_deg 1.754 r_mcangle_it 1.684 r_angle_other_deg 1.388 r_mcbond_it 1.043 r_chiral_restr 0.11 r_bond_refined_d 0.023 r_gen_planes_other 0.013 r_gen_planes_refined 0.01 r_bond_other_d 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_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2082 Nucleic Acid Atoms Solvent Atoms 237 Heterogen Atoms 6
Software Software Software Name Purpose MOLREP phasing REFMAC refinement XDS data reduction XDS data scaling