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Crystal structure of the Type-I signal peptidase from Staphylococcus aureus (SpsB) in complex with a substrate peptide (pep1).
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 296 12 % PEG 8000, 20 % ethylene glycol, 100 mM sodium acetate pH 5.3 - 5.5
Crystal Properties Matthews coefficient Solvent content 2.62 53.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.661 α = 90 b = 80.193 β = 90 c = 119.426 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 210r 2014-06-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX1 0.9537 Australian Synchrotron MX1
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 2.1 66.58 99.9 0.319 0.086 0.994 10 36431
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 2.1 2.16 100 2.622 0.703 0.589 1.6 14.8 2945
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 2.1 66.58 34573 1799 99.81 0.2103 0.2083 0.2161 0.2485 0.2532 RANDOM 29.051
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] 0.29 -0.88 0.59
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.396 r_dihedral_angle_3_deg 13.308 r_dihedral_angle_4_deg 7.955 r_dihedral_angle_1_deg 5.635 r_mcangle_it 2.028 r_mcbond_it 1.227 r_mcbond_other 1.227 r_angle_refined_deg 1.174 r_angle_other_deg 0.725 r_chiral_restr 0.066
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.396 r_dihedral_angle_3_deg 13.308 r_dihedral_angle_4_deg 7.955 r_dihedral_angle_1_deg 5.635 r_mcangle_it 2.028 r_mcbond_it 1.227 r_mcbond_other 1.227 r_angle_refined_deg 1.174 r_angle_other_deg 0.725 r_chiral_restr 0.066 r_bond_refined_d 0.007 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 246 Heterogen Atoms 23
Software Software Software Name Purpose REFMAC refinement XDS data scaling Aimless data scaling PHASER phasing PDB_EXTRACT data extraction