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Structure of V8 protease from staphylococcus aureus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1QY6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.6 293 PEG 5000 MME, KCl, HEPES, pH 8.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 1.84 33.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.43 α = 90 b = 59.43 β = 90 c = 214.01 γ = 120
Symmetry Space Group P 65 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray CCD MARMOSAIC 225 mm CCD 2006-08-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08ID-1 1.3317 CLSI 08ID-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 1.5 19.4 89.8 0.13 0.14 9.95 5.94 65067 58412 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) 1.5 1.63 92.3 0.418 0.471 3.2 4 11330
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 (All) 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 1QY6 1.5 19.37 32179 32179 1694 100 0.1899 0.1899 0.18839 0.1869 0.21867 0.2171 RANDOM 10.418
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] 0.03 0.02 0.03 -0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.873 r_dihedral_angle_4_deg 26.411 r_dihedral_angle_3_deg 13.92 r_dihedral_angle_1_deg 6.853 r_scangle_it 5.407 r_scbond_it 3.509 r_angle_refined_deg 2.366 r_mcangle_it 2.084 r_mcbond_it 1.251 r_metal_ion_refined 0.838
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.873 r_dihedral_angle_4_deg 26.411 r_dihedral_angle_3_deg 13.92 r_dihedral_angle_1_deg 6.853 r_scangle_it 5.407 r_scbond_it 3.509 r_angle_refined_deg 2.366 r_mcangle_it 2.084 r_mcbond_it 1.251 r_metal_ion_refined 0.838 r_symmetry_metal_ion_refined 0.583 r_symmetry_vdw_refined 0.477 r_nbtor_refined 0.338 r_nbd_refined 0.263 r_chiral_restr 0.187 r_xyhbond_nbd_refined 0.176 r_symmetry_hbond_refined 0.172 r_bond_refined_d 0.028 r_gen_planes_refined 0.013
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1653 Nucleic Acid Atoms Solvent Atoms 152 Heterogen Atoms 1
Software Software Software Name Purpose AMoRE phasing REFMAC refinement XDS data reduction XDS data scaling