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The crystal structure of the complex of Streptococcus agalactiae sortase C1 and MTSET
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3TB7 PDB ENTRY 3TB7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 277 1.6 M ammonium sulfate, 5% PEG3350, 0.446 M sodium cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.72 54.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 122.41 α = 90 b = 70.65 β = 90.43 c = 194.44 γ = 90
Symmetry Space Group C 1 2 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 IMAGE PLATE RIGAKU RAXIS IV 2009-08-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.541
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 2.85 196.116 99.6 0.06 11.1 3.45 39189 38964
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.85 2.95 100 0.331 3 3.57
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 PDB ENTRY 3TB7 2.85 27.707 36974 1956 99.34 0.25266 0.25033 0.2455 0.29604 0.2913 RANDOM 51.923
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] 0.5 0.05 -0.14 -0.36
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.299 r_dihedral_angle_3_deg 19.865 r_dihedral_angle_4_deg 18.956 r_dihedral_angle_1_deg 7.021 r_scangle_it 3.761 r_scbond_it 2.072 r_mcangle_it 2.017 r_angle_refined_deg 1.617 r_mcbond_it 1.068 r_chiral_restr 0.102
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.299 r_dihedral_angle_3_deg 19.865 r_dihedral_angle_4_deg 18.956 r_dihedral_angle_1_deg 7.021 r_scangle_it 3.761 r_scbond_it 2.072 r_mcangle_it 2.017 r_angle_refined_deg 1.617 r_mcbond_it 1.068 r_chiral_restr 0.102 r_bond_refined_d 0.015 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8832 Nucleic Acid Atoms Solvent Atoms 108 Heterogen Atoms 68
Software Software Software Name Purpose REFMAC refinement PHASER phasing CNS refinement StructureStudio data collection d*TREK data reduction d*TREK data scaling