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Crystal structure of Escherichia coli Signal peptide peptidase (SppA), SeMet crystals
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 291 PEG3350, pH 7.5, vapor diffusion, hanging drop, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.68 54.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.022 α = 90 b = 153.04 β = 104.17 c = 100.214 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 mirrors M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X4A 0.97925 NSLS X4A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 2.76 46.9 97.8 0.178 0.178 15.6 7.4 69169
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.76 2.9 78 0.45 0.33 3.3 6.1 5523
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 SAD THROUGHOUT 2.76 46.63 69168 3502 100 0.203 0.2 0.259 0.2236 RANDOM 25.373
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] 1.98 2.51 -1.84 1.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.429 r_dihedral_angle_3_deg 20.497 r_dihedral_angle_4_deg 18.842 r_dihedral_angle_1_deg 10.396 r_scangle_it 3.619 r_scbond_it 2.238 r_angle_refined_deg 1.892 r_mcangle_it 1.361 r_mcbond_it 0.868 r_nbtor_refined 0.324
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.429 r_dihedral_angle_3_deg 20.497 r_dihedral_angle_4_deg 18.842 r_dihedral_angle_1_deg 10.396 r_scangle_it 3.619 r_scbond_it 2.238 r_angle_refined_deg 1.892 r_mcangle_it 1.361 r_mcbond_it 0.868 r_nbtor_refined 0.324 r_nbd_refined 0.252 r_symmetry_vdw_refined 0.189 r_xyhbond_nbd_refined 0.169 r_symmetry_hbond_refined 0.155 r_chiral_restr 0.129 r_bond_refined_d 0.017 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 14362 Nucleic Acid Atoms Solvent Atoms 627 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling SHELX phasing RESOLVE phasing REFMAC refinement PDB_EXTRACT data extraction SHELXD phasing