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Crystal Structure of Sortase C-3 (SRTC-3) from Streptococcus pneumoniae
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2W1J PDB ENTRY 2W1J
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5 100 MM MES PH 5.0, 0.5 M (NH4)2SO4, 1.0 M LISO4
Crystal Properties Matthews coefficient Solvent content 2.41 48.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 122.638 α = 90 b = 122.638 β = 90 c = 122.638 γ = 90
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 IMAGE PLATE 2008-03-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU ROTAFLEX
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2.14 43.35 90.8 0.1 14.3 6.6 31007 3 35.09
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 2.14 2.27 76.3 0.52 4.2 6
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 2W1J 2.14 43.35 32021 1674 100 0.183 0.18 0.1864 0.241 0.2458 RANDOM 37.68
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.436 r_dihedral_angle_4_deg 21.207 r_dihedral_angle_3_deg 15.988 r_dihedral_angle_1_deg 7.975 r_scangle_it 5.459 r_scbond_it 3.837 r_mcangle_it 2.474 r_angle_refined_deg 2.296 r_angle_other_deg 2.296 r_mcbond_it 1.457
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.436 r_dihedral_angle_4_deg 21.207 r_dihedral_angle_3_deg 15.988 r_dihedral_angle_1_deg 7.975 r_scangle_it 5.459 r_scbond_it 3.837 r_mcangle_it 2.474 r_angle_refined_deg 2.296 r_angle_other_deg 2.296 r_mcbond_it 1.457 r_chiral_restr 0.225 r_bond_refined_d 0.028 r_bond_other_d 0.028 r_gen_planes_refined 0.012 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_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3296 Nucleic Acid Atoms Solvent Atoms 505 Heterogen Atoms 24
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing