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Crystal structure of Escherichia coli Signal peptide peptidase (SppA), Native 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 2.76 55.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 94.171 α = 90 b = 153.485 β = 104.25 c = 100.659 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 2.5 50 96.2 0.122 0.122 16 7.2 86579 86579
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) 2.5 2.6 80.8 0.324 0.32 3.2 6 7232
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.55 50 86551 4338 96.16 0.217 0.214 0.2082 0.252 0.2635 RANDOM 28.947
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] 2.3 1.8 -1.84 0.43
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.861 r_dihedral_angle_3_deg 19.427 r_dihedral_angle_4_deg 17.424 r_dihedral_angle_1_deg 7.726 r_scangle_it 3.586 r_scbond_it 2.196 r_angle_refined_deg 1.765 r_mcangle_it 1.474 r_mcbond_it 0.877 r_nbtor_refined 0.314
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.861 r_dihedral_angle_3_deg 19.427 r_dihedral_angle_4_deg 17.424 r_dihedral_angle_1_deg 7.726 r_scangle_it 3.586 r_scbond_it 2.196 r_angle_refined_deg 1.765 r_mcangle_it 1.474 r_mcbond_it 0.877 r_nbtor_refined 0.314 r_nbd_refined 0.232 r_xyhbond_nbd_refined 0.156 r_symmetry_vdw_refined 0.152 r_chiral_restr 0.122 r_symmetry_hbond_refined 0.094 r_bond_refined_d 0.016 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 14377 Nucleic Acid Atoms Solvent Atoms 488 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction