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The antimicrobial peptidase lysostaphin from Staphylococcus simulans
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1R77 pdb entries 1R77, 2B0P experimental model PDB 2B0P pdb entries 1R77, 2B0P
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 277 0.1 M MES and 1.6 M magnesium sulphate, 2 mM tetraglycine phosphinic acid. EDTA and ammonium sulphate as additives improved crystal quality, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 8.29 85.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 282.013 α = 90 b = 282.013 β = 90 c = 282.013 γ = 90
Symmetry Space Group P 43 3 2
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 2013-02-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.918409 BESSY 14.1
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 3.5 50 100 0.295 0.295 17.34 36.4 48693 48693 36.3
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 3.5 3.59 100 0.908 0.908 5.34 37.9 3539
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT pdb entries 1R77, 2B0P 3.5 47.67 48689 48689 2435 100 0.26873 0.26777 0.28684 0.2295 RANDOM 40.566
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 36.969 r_dihedral_angle_3_deg 17.977 r_dihedral_angle_4_deg 9.819 r_dihedral_angle_1_deg 6.457 r_angle_other_deg 4.421 r_angle_refined_deg 1.193 r_symmetry_vdw_other 0.252 r_nbd_other 0.231 r_symmetry_vdw_refined 0.225 r_nbd_refined 0.211
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.969 r_dihedral_angle_3_deg 17.977 r_dihedral_angle_4_deg 9.819 r_dihedral_angle_1_deg 6.457 r_angle_other_deg 4.421 r_angle_refined_deg 1.193 r_symmetry_vdw_other 0.252 r_nbd_other 0.231 r_symmetry_vdw_refined 0.225 r_nbd_refined 0.211 r_nbtor_refined 0.195 r_metal_ion_refined 0.182 r_xyhbond_nbd_refined 0.157 r_symmetry_hbond_refined 0.142 r_nbtor_other 0.118 r_chiral_restr 0.066 r_gen_planes_other 0.035 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_bond_other_d r_xyhbond_nbd_other r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it 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 7540 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 49
Software Software Software Name Purpose CBFlib data collection PHASER phasing REFMAC refinement XDS data reduction XSCALE data scaling