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Crystal structure of sortase A from Streptococcus pyogenes serotype M1 strain SF370 with the active site Cys in its sulphenic acid form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1T2P PDB entry 1T2P
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 2.24 45.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.951 α = 90 b = 69.799 β = 90 c = 39.867 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++ 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 1.9 26.26 100 0.064 19.7 4.7 15111 15111
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) 1.9 2 100 0.258 5.3 4.7 2170
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 1T2P 1.9 26.26 14325 14325 761 99.92 0.1894 0.1894 0.18743 0.191 0.22728 0.2319 RANDOM 17.82
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] -1.89 -0.86 2.75
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.241 r_dihedral_angle_4_deg 15.519 r_dihedral_angle_3_deg 15.226 r_dihedral_angle_1_deg 6.364 r_scangle_it 4.023 r_scbond_it 2.481 r_mcangle_it 1.745 r_angle_refined_deg 1.592 r_mcbond_it 0.993 r_angle_other_deg 0.9
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.241 r_dihedral_angle_4_deg 15.519 r_dihedral_angle_3_deg 15.226 r_dihedral_angle_1_deg 6.364 r_scangle_it 4.023 r_scbond_it 2.481 r_mcangle_it 1.745 r_angle_refined_deg 1.592 r_mcbond_it 0.993 r_angle_other_deg 0.9 r_mcbond_other 0.245 r_chiral_restr 0.091 r_bond_refined_d 0.017 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.001 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1345 Nucleic Acid Atoms Solvent Atoms 159 Heterogen Atoms
Software Software Software Name Purpose CrystalClear data collection PHASER phasing REFMAC refinement MOSFLM data reduction SCALA data scaling