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Crystal structure of housekeeping sortase SrtA bound with self derived tripeptide from Lactobacillus rhamnosus GG
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3FN5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 295 0.05 M Citric Bis-Tris Propane, pH 5.0 and 16% (w/v) PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.13 42.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 34.608 α = 90 b = 55.674 β = 103.22 c = 75.312 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 MARMOSAIC 225 mm CCD 2016-02-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 0.97934 ESRF BM14
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.686 73.32 90 0.103 0.061 0.998 9.9 3.8 23044
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.686 1.865 1.151 0.674 0.476 1.3
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 3FN5 1.69 73.32 21908 1135 73 0.18307 0.18139 0.1915 0.21368 0.2176 RANDOM 25.939
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] 0.11 -0.03 -0.04 -0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.496 r_dihedral_angle_3_deg 13.292 r_long_range_B_refined 9.211 r_long_range_B_other 9.186 r_dihedral_angle_4_deg 8.184 r_scangle_other 7.433 r_dihedral_angle_1_deg 5.788 r_scbond_it 4.996 r_scbond_other 4.994 r_mcangle_it 4.434
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.496 r_dihedral_angle_3_deg 13.292 r_long_range_B_refined 9.211 r_long_range_B_other 9.186 r_dihedral_angle_4_deg 8.184 r_scangle_other 7.433 r_dihedral_angle_1_deg 5.788 r_scbond_it 4.996 r_scbond_other 4.994 r_mcangle_it 4.434 r_mcangle_other 4.433 r_mcbond_it 3.067 r_mcbond_other 3.057 r_angle_refined_deg 1.315 r_angle_other_deg 0.999 r_chiral_restr 0.072 r_bond_refined_d 0.008 r_gen_planes_refined 0.004 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 2252 Nucleic Acid Atoms Solvent Atoms 161 Heterogen Atoms 29
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing