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Structure of IdeC protease C94S from Streptococcus canis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1Y08
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 30% PEG 3350, 200 mM MgCl2 and 100 mM Tris HCl pH 8.5
Crystal Properties Matthews coefficient Solvent content 2.07 40.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.253 α = 90 b = 70.253 β = 90 c = 94.884 γ = 120
Symmetry Space Group P 32 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 PIXEL DECTRIS PILATUS 6M 2019-10-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.979 ALBA XALOC
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.7 47.44 99.9 0.138 0.977 4.8 9.5 7819
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.7 2.83 100 0.792 0.447 1 9.5
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.7 37.44 7793 360 99.872 0.205 0.2017 0.2051 0.2675 0.2706 48.865
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] 1.354 0.677 1.354 -4.391
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.653 r_dihedral_angle_6_deg 14.355 r_lrange_it 6.997 r_lrange_other 6.976 r_dihedral_angle_1_deg 6.07 r_scangle_it 4.783 r_scangle_other 4.706 r_mcangle_it 4.451 r_mcangle_other 4.449 r_scbond_it 2.825
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.653 r_dihedral_angle_6_deg 14.355 r_lrange_it 6.997 r_lrange_other 6.976 r_dihedral_angle_1_deg 6.07 r_scangle_it 4.783 r_scangle_other 4.706 r_mcangle_it 4.451 r_mcangle_other 4.449 r_scbond_it 2.825 r_scbond_other 2.769 r_mcbond_it 2.646 r_mcbond_other 2.644 r_dihedral_angle_2_deg 2.303 r_angle_refined_deg 1.08 r_angle_other_deg 0.393 r_symmetry_nbd_other 0.211 r_nbd_refined 0.21 r_nbd_other 0.203 r_symmetry_nbd_refined 0.199 r_nbtor_refined 0.18 r_symmetry_xyhbond_nbd_refined 0.16 r_xyhbond_nbd_refined 0.158 r_symmetry_nbtor_other 0.078 r_chiral_restr 0.05 r_symmetry_xyhbond_nbd_other 0.048 r_bond_refined_d 0.004 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2305 Nucleic Acid Atoms Solvent Atoms 32 Heterogen Atoms 25
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing