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1.8 Angstrom Crystal Structure of Signal Peptidase I from Bacillus anthracis.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4ME8 PDB ENTRY 4ME8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.3 295 Protein: 7.3 mG/mL, 0.25 M Sodium chloride, 0.01 M Tris-HCL buffer pH 8.3;
Screen: Classics II (H11), 0.1M Potassium thiocyanate, 30% (w/v) PEG 2000 MME., VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2 38.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.225 α = 90 b = 80.225 β = 90 c = 174.25 γ = 120
Symmetry Space Group P 63 2 2
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 MARMOSAIC 225 mm CCD Beryllium lenses 2013-11-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
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 1.8 30 99.8 0.056 0.056 30 7.1 31574 31574 -3 27.2
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 1.8 1.83 100 0.512 0.512 3.9 7.2 1542
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 (All) 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 PDB ENTRY 4ME8 1.8 29.81 29946 29946 1591 99.76 0.17403 0.17403 0.17272 0.1994 0.2229 RANDOM 35.616
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] 0.56 0.28 0.56 -1.82
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.514 r_dihedral_angle_4_deg 12.077 r_dihedral_angle_3_deg 11.49 r_long_range_B_refined 7.609 r_long_range_B_other 7.514 r_scangle_other 4.628 r_dihedral_angle_1_deg 4.454 r_scbond_it 3.007 r_scbond_other 3.001 r_mcangle_other 2.85
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.514 r_dihedral_angle_4_deg 12.077 r_dihedral_angle_3_deg 11.49 r_long_range_B_refined 7.609 r_long_range_B_other 7.514 r_scangle_other 4.628 r_dihedral_angle_1_deg 4.454 r_scbond_it 3.007 r_scbond_other 3.001 r_mcangle_other 2.85 r_mcangle_it 2.849 r_mcbond_it 1.88 r_mcbond_other 1.87 r_angle_refined_deg 1.558 r_angle_other_deg 0.736 r_chiral_restr 0.114 r_bond_refined_d 0.011 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1865 Nucleic Acid Atoms Solvent Atoms 206 Heterogen Atoms 61
Software Software Software Name Purpose Blu-Ice data collection PHASER phasing REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling