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Atomic resolution structure of SplF protease from Staphylococcus aureus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other Other 4VID
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 32.5 % PEG 400, 0.3 M Ammonium Sulphate pH = 3.5
Crystal Properties Matthews coefficient Solvent content 2.31 46.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56 α = 104.57 b = 58.58 β = 95.31 c = 62.3 γ = 90.6
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 RIGAKU RAXIS IV++ 2011-05-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.54
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.7 30 92.6 0.047 6.4 3.6 77687
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.7 1.79 88.8 0.11 13.9 3.7
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 4VID 1.7 29.84 73794 3888 92.54 0.1694 0.1674 0.1765 0.2078 0.2145 RANDOM 27.698
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] 0.6 -0.68 -0.34 -0.28 -0.14 -0.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.628 r_dihedral_angle_4_deg 23.379 r_dihedral_angle_3_deg 13.163 r_dihedral_angle_1_deg 7.18 r_angle_refined_deg 2.05 r_angle_other_deg 1.583 r_chiral_restr 0.112 r_bond_refined_d 0.017 r_gen_planes_refined 0.014 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.628 r_dihedral_angle_4_deg 23.379 r_dihedral_angle_3_deg 13.163 r_dihedral_angle_1_deg 7.18 r_angle_refined_deg 2.05 r_angle_other_deg 1.583 r_chiral_restr 0.112 r_bond_refined_d 0.017 r_gen_planes_refined 0.014 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5897 Nucleic Acid Atoms Solvent Atoms 451 Heterogen Atoms 115
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction iMOSFLM data reduction SCALA data scaling PHASER phasing