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Crystal structure of the Type-I signal peptidase from Staphylococcus aureus (SpsB) in complex with a substrate peptide (pep2).
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4WVG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 BATCH MODE 290 12 % PEG 8000, 20 % ethylene glycol, 100 mM sodium acetate pH 5.3 - 5.5
Crystal Properties Matthews coefficient Solvent content 2.63 53.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.989 α = 90 b = 80.232 β = 90 c = 119.879 γ = 90
Symmetry Space Group P 21 21 21
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 ADSC QUANTUM 315r 2014-04-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.9537 Australian Synchrotron MX2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) 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 1.9 19.78 99.9 0.19 0.064 0.997 11.1 9.5 49376
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 1.94 100 2.077 0.698 0.514 1.5 9.5 3283
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 4WVG 1.9 19.78 46809 2503 99.83 0.1895 0.1879 0.1961 0.2194 0.2255 RANDOM 24.36
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] 0.37 -0.6 0.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.15 r_dihedral_angle_4_deg 13.638 r_dihedral_angle_3_deg 12.378 r_dihedral_angle_1_deg 5.633 r_mcangle_it 2.074 r_mcbond_it 1.275 r_mcbond_other 1.27 r_angle_refined_deg 1.215 r_angle_other_deg 0.741 r_chiral_restr 0.072
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.15 r_dihedral_angle_4_deg 13.638 r_dihedral_angle_3_deg 12.378 r_dihedral_angle_1_deg 5.633 r_mcangle_it 2.074 r_mcbond_it 1.275 r_mcbond_other 1.27 r_angle_refined_deg 1.215 r_angle_other_deg 0.741 r_chiral_restr 0.072 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4075 Nucleic Acid Atoms Solvent Atoms 371 Heterogen Atoms 23
Software Software Software Name Purpose XDS data scaling Aimless data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction