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Crystal structure of sortase A (Spy1154) from Streptococcus pyogenes serotype M1 strain SF370
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3FN6 PDB entry 3FN6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 100 mM Tris (pH 6 - 7), 20 30 % (w/v) polyethyleneglycol (PEG) 8000 and 200 mM sodium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.26 45.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.03 α = 90 b = 69.89 β = 90 c = 40.15 γ = 90
Symmetry Space Group P 21 21 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 IMAGE PLATE RIGAKU RAXIS IV++ Osmic mirrors 2007-07-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 1.54
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.7 29.85 100 0.058 27.6 13.4 21140 21140 25.6
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.7 1.79 100 0.379 5.6 12.4 3039
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 3FN6 1.75 29.85 18391 18391 967 99.96 0.19846 0.19846 0.19638 0.23891 0.2525 RANDOM 28.552
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] -1.85 -1.2 3.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.87 r_dihedral_angle_4_deg 25.03 r_dihedral_angle_3_deg 12.794 r_sphericity_free 7.306 r_dihedral_angle_1_deg 6.115 r_sphericity_bonded 4.897 r_scangle_it 4.518 r_scbond_it 3.164 r_mcangle_it 2.192 r_rigid_bond_restr 2.145
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.87 r_dihedral_angle_4_deg 25.03 r_dihedral_angle_3_deg 12.794 r_sphericity_free 7.306 r_dihedral_angle_1_deg 6.115 r_sphericity_bonded 4.897 r_scangle_it 4.518 r_scbond_it 3.164 r_mcangle_it 2.192 r_rigid_bond_restr 2.145 r_angle_refined_deg 1.548 r_mcbond_it 1.4 r_chiral_restr 0.107 r_bond_refined_d 0.016 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1411 Nucleic Acid Atoms Solvent Atoms 108 Heterogen Atoms
Software Software Software Name Purpose CrystalClear data collection PHASER phasing REFMAC refinement MOSFLM data reduction SCALA data scaling