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SrtA sortase from Actinomyces oris
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5CUW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.6 289 25% PEG 3350, 0.2 M magnesium chloride, 0.1 M Bis-Tris:HCl buffer
Crystal Properties Matthews coefficient Solvent content 2.17 43.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.183 α = 90 b = 75.085 β = 89.96 c = 77.652 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 210r 2017-02-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-BM 0.9792 APS 19-BM
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 37.54 94.9 0.078 0.092 0.048 10.6 3.6 74465 15
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.7 1.73 75.3 0.619 0.742 0.404 0.801 1.92 2.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 5CUW 1.7 37.54 70787 3651 94.67 0.16202 0.15988 0.1665 0.20454 0.2128 RANDOM 18.422
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] -17.99 0.29 25.41 -7.42
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.292 r_dihedral_angle_4_deg 14.029 r_dihedral_angle_3_deg 12.24 r_dihedral_angle_1_deg 6.494 r_long_range_B_refined 4.694 r_long_range_B_other 4.56 r_scangle_other 2.015 r_angle_refined_deg 1.422 r_mcangle_it 1.38 r_mcangle_other 1.38
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.292 r_dihedral_angle_4_deg 14.029 r_dihedral_angle_3_deg 12.24 r_dihedral_angle_1_deg 6.494 r_long_range_B_refined 4.694 r_long_range_B_other 4.56 r_scangle_other 2.015 r_angle_refined_deg 1.422 r_mcangle_it 1.38 r_mcangle_other 1.38 r_scbond_it 1.26 r_scbond_other 1.26 r_mcbond_other 0.85 r_mcbond_it 0.849 r_angle_other_deg 0.812 r_chiral_restr 0.087 r_bond_refined_d 0.012 r_gen_planes_refined 0.007 r_bond_other_d 0.001 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5620 Nucleic Acid Atoms Solvent Atoms 529 Heterogen Atoms 12
Software Software Software Name Purpose REFMAC refinement HKL-3000 data scaling PDB_EXTRACT data extraction HKL-3000 data reduction HKL-3000 phasing MOLREP phasing DENZO data reduction SCALEPACK data scaling