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Crystal structure of Bacillus subtilis signal peptide peptidase A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3BFO 3BFO , Chain A, C-terminal Domain (residues 326-549)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 291.15 100mM Tris pH 8.5
23% Tert-butanol
5% MPD, VAPOR DIFFUSION, SITTING DROP, temperature 291.15K
Crystal Properties Matthews coefficient Solvent content 2.67 54.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.779 α = 90 b = 131.066 β = 90 c = 207.263 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 RAYONIX MX-300 vertical collimating mirror 2011-02-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08ID-1 0.97949 CLSI 08ID-1
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 2.37 50 99.8 0.085 52.7 7.4 96535 96535 2 -3
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 2.37 2.49 99.8 0.294 7.8 6.9
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 (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 3BFO , Chain A, C-terminal Domain (residues 326-549) 2.37 50 95998 91450 4806 98.16 0.20748 0.20571 0.1999 0.24052 0.2335 RANDOM 48.998
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] -0.34 1.1 -0.76
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.545 r_dihedral_angle_3_deg 16.322 r_dihedral_angle_4_deg 13.573 r_dihedral_angle_1_deg 5.31 r_scangle_it 2.736 r_scbond_it 1.648 r_angle_refined_deg 1.135 r_mcangle_it 0.888 r_mcbond_it 0.443 r_chiral_restr 0.074
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.545 r_dihedral_angle_3_deg 16.322 r_dihedral_angle_4_deg 13.573 r_dihedral_angle_1_deg 5.31 r_scangle_it 2.736 r_scbond_it 1.648 r_angle_refined_deg 1.135 r_mcangle_it 0.888 r_mcbond_it 0.443 r_chiral_restr 0.074 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13685 Nucleic Acid Atoms Solvent Atoms 257 Heterogen Atoms
Software Software Software Name Purpose MxDC data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling