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Crystal structure of the Type-I signal peptidase from Staphylococcus aureus (SpsB).
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ANF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 296 12 % PEG 8000, 20 % ethylene glycol, 0.2 M amino acids mix (0.2 M sodium-L-glutamate, 0.2 M DL-alanine, 0.2 M glycine, 0.2 M DL-lysine, 0.2 M DL-serine), 100 mM Tris.Cl pH 8.5
Crystal Properties Matthews coefficient Solvent content 2.43 49.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.683 α = 90 b = 63.565 β = 92.59 c = 79.892 γ = 90
Symmetry Space Group P 1 21 1
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 2013-03-25 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 2.05 19.44 99.8 0.211 0.082 0.994 10.1 7.6 36318
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 2.05 2.11 99.8 1.577 0.608 0.528 1.4 7.6 2779
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1ANF 2.05 19.44 34468 1839 99.72 0.1921 0.1896 0.242 0.1919 RANDOM 29.325
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] -0.72 -0.32 -0.51 1.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.687 r_dihedral_angle_3_deg 12.969 r_dihedral_angle_4_deg 8.241 r_dihedral_angle_1_deg 5.331 r_mcangle_it 2.211 r_mcbond_it 1.296 r_mcbond_other 1.296 r_angle_refined_deg 1.16 r_angle_other_deg 0.717 r_chiral_restr 0.066
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.687 r_dihedral_angle_3_deg 12.969 r_dihedral_angle_4_deg 8.241 r_dihedral_angle_1_deg 5.331 r_mcangle_it 2.211 r_mcbond_it 1.296 r_mcbond_other 1.296 r_angle_refined_deg 1.16 r_angle_other_deg 0.717 r_chiral_restr 0.066 r_bond_refined_d 0.007 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 3977 Nucleic Acid Atoms Solvent Atoms 356 Heterogen Atoms 23
Software Software Software Name Purpose XDS data scaling Aimless data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction