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The crystal structure of SrtC2 sortase from Actinomyces oris
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2XWG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.2 277 0.2 M Sodium Chloride, 0.1 M Na2HPO4:Citric Acid, 20% (w/v) PEG 8000
Crystal Properties Matthews coefficient Solvent content 2.5 50.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.39 α = 90 b = 90.39 β = 90 c = 101.704 γ = 120
Symmetry Space Group P 62 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 PIXEL DECTRIS PILATUS3 X 6M 2017-12-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.9792 APS 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 2.1 45.24 99.7 0.124 0.127 0.027 0.998 5.4 20.2 14868
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 2.1 2.14 96.8 1.156 1.257 0.461 0.504 1.08 6.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.1 45.24 14075 764 99.74 0.16861 0.16688 0.1801 0.20098 0.2133 RANDOM 37.069
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] 0.12 0.06 0.12 -0.39
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.283 r_dihedral_angle_1_deg 7.086 r_long_range_B_refined 6.756 r_long_range_B_other 6.719 r_dihedral_angle_2_deg 6.036 r_scangle_other 5.532 r_scbond_it 3.829 r_scbond_other 3.792 r_mcangle_it 3.089 r_mcangle_other 3.088
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.283 r_dihedral_angle_1_deg 7.086 r_long_range_B_refined 6.756 r_long_range_B_other 6.719 r_dihedral_angle_2_deg 6.036 r_scangle_other 5.532 r_scbond_it 3.829 r_scbond_other 3.792 r_mcangle_it 3.089 r_mcangle_other 3.088 r_mcbond_it 2.253 r_mcbond_other 2.253 r_angle_refined_deg 1.591 r_angle_other_deg 0.491 r_chiral_restr 0.065 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg 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 1390 Nucleic Acid Atoms Solvent Atoms 108 Heterogen Atoms 12
Software Software Software Name Purpose REFMAC refinement HKL-3000 data scaling HKL-3000 data reduction HKL-3000 phasing