☰ Navigation Tabs
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 1.82 32.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.28 α = 90 b = 59.46 β = 101.96 c = 65.11 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 QUANTUM 315 2007-11-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.5 32.27 94.7 0.078 12.9 3.3 44430 44430 17.1
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) 1.5 1.54 93.7 0.34 2.7 3.4 6387
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 3FN6 1.5 32.27 42151 42151 2260 94.39 0.14808 0.14808 0.1458 0.1541 0.19027 0.1962 RANDOM 14.132
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] 1.3 1.91 -0.48 -0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.755 r_dihedral_angle_3_deg 12.428 r_dihedral_angle_4_deg 12.07 r_sphericity_free 7.112 r_dihedral_angle_1_deg 5.666 r_scangle_it 4.547 r_sphericity_bonded 3.708 r_scbond_it 3.149 r_mcangle_it 2.334 r_angle_refined_deg 1.585
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.755 r_dihedral_angle_3_deg 12.428 r_dihedral_angle_4_deg 12.07 r_sphericity_free 7.112 r_dihedral_angle_1_deg 5.666 r_scangle_it 4.547 r_sphericity_bonded 3.708 r_scbond_it 3.149 r_mcangle_it 2.334 r_angle_refined_deg 1.585 r_rigid_bond_restr 1.531 r_mcbond_it 1.528 r_angle_other_deg 1.02 r_mcbond_other 0.69 r_chiral_restr 0.101 r_bond_refined_d 0.016 r_gen_planes_refined 0.007 r_gen_planes_other 0.002 r_bond_other_d 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2536 Nucleic Acid Atoms Solvent Atoms 351 Heterogen Atoms 15
Software Software Software Name Purpose ADSC data collection PHASER phasing REFMAC refinement MOSFLM data reduction SCALA data scaling