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2.05 Angstrom Resolution Crystal Structure of Epidermin Leader Peptide Processing Serine Protease (EpiP) from Staphylococcus aureus.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1THM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 295 Protein: 7mg/mL, ?M Sodium cloride, Tris-HCl (pH 8.3), Screen: GCSG+ (H9), 0.2M Lithium sulfate, 0.1M Bis-Tris pH 5.5, 25% (w/v) PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.22 44.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.505 α = 89.98 b = 94.696 β = 90.37 c = 122.999 γ = 116.79
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MARMOSAIC 225 mm CCD Beryllium lenses 2010-11-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
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 2.05 30 97.9 0.047 15 2 219399 219399 -3 30.9
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) 2.05 2.09 97 0.354 2.1 2 10837
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 1THM 2.05 29.69 200752 200752 10599 97.82 0.1718 0.1718 0.1695 0.1824 0.21596 0.2303 RANDOM 38.607
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] -1.78 -2.15 -0.19 1.41 0.13 -1.57
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.189 r_dihedral_angle_4_deg 10.99 r_dihedral_angle_3_deg 10.394 r_scangle_it 4.668 r_dihedral_angle_1_deg 3.107 r_scbond_it 2.976 r_mcangle_it 1.797 r_angle_refined_deg 1.353 r_mcbond_it 1.018 r_angle_other_deg 0.834
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.189 r_dihedral_angle_4_deg 10.99 r_dihedral_angle_3_deg 10.394 r_scangle_it 4.668 r_dihedral_angle_1_deg 3.107 r_scbond_it 2.976 r_mcangle_it 1.797 r_angle_refined_deg 1.353 r_mcbond_it 1.018 r_angle_other_deg 0.834 r_mcbond_other 0.297 r_chiral_restr 0.085 r_bond_refined_d 0.011 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 26598 Nucleic Acid Atoms Solvent Atoms 1511 Heterogen Atoms 221
Software Software Software Name Purpose Blu-Ice data collection PHASER phasing REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling