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Structural, biophysical and biochemical analyses of a Clostridium perfringens Sortase D5 transpeptidase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3G66 PDB ENTRY 3G66
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 5.5 281 THE PROTEIN CONCENTRATION WAS 20 MG/ML AND THE RESERVOIR CONDITIONS WERE 0.2M AMMONIUM ACETATE, 25% PEG 3350, 0.1M BIS-TRIS CHLORIDE AT PH 5.5 AND INCUBATED AT 8C.
Crystal Properties Matthews coefficient Solvent content 2.41 48.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.776 α = 90 b = 65.582 β = 93.86 c = 68.057 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 CCD 2013-06-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 Australian Synchrotron MX2
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 1.99 47.2 99.5 0.07 18 7.5 23533
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 1.99 2.09 97.1 0.63 3.2 7
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 3G66 1.99 67.9 22304 1214 99.5 0.17769 0.17569 0.1835 0.21335 0.217 RANDOM 38.509
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] 1.08 0.4 -0.85 -0.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.917 r_dihedral_angle_3_deg 14.053 r_dihedral_angle_4_deg 8.386 r_long_range_B_refined 8.33 r_long_range_B_other 8.322 r_scangle_other 7.437 r_dihedral_angle_1_deg 5.745 r_scbond_it 5.16 r_scbond_other 5.158 r_mcangle_it 4.474
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.917 r_dihedral_angle_3_deg 14.053 r_dihedral_angle_4_deg 8.386 r_long_range_B_refined 8.33 r_long_range_B_other 8.322 r_scangle_other 7.437 r_dihedral_angle_1_deg 5.745 r_scbond_it 5.16 r_scbond_other 5.158 r_mcangle_it 4.474 r_mcangle_other 4.474 r_mcbond_other 3.527 r_mcbond_it 3.526 r_angle_refined_deg 1.687 r_angle_other_deg 1.227 r_chiral_restr 0.11 r_bond_refined_d 0.016 r_gen_planes_refined 0.009 r_bond_other_d 0.006 r_gen_planes_other 0.005 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 2526 Nucleic Acid Atoms Solvent Atoms 95 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling PHASER phasing