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Structure of the truncated version 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 6.5 291 20% PEG 3350, 200 mM Na/K phosphate, and 100 mM Bis Tris propane pH 6.5
Crystal Properties Matthews coefficient Solvent content 3.36 63.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 109.379 α = 90 b = 109.379 β = 90 c = 109.379 γ = 90
Symmetry Space Group P 21 3
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 2020-06-12 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 2.25 48.96 100 0.059 0.997 11.3 12.6 21011
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 2.25 2.32 100 0.706 0.431 1.2 12.7
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 (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.25 48.96 19931 1057 99.99 0.18004 0.17819 0.21374 0.1965 RANDOM 40.17
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 40.561 r_dihedral_angle_4_deg 17.336 r_dihedral_angle_3_deg 16.295 r_long_range_B_other 9.329 r_long_range_B_refined 9.318 r_dihedral_angle_1_deg 7.159 r_scangle_other 7.072 r_mcangle_it 6.064 r_mcangle_other 6.062 r_scbond_it 4.547
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.561 r_dihedral_angle_4_deg 17.336 r_dihedral_angle_3_deg 16.295 r_long_range_B_other 9.329 r_long_range_B_refined 9.318 r_dihedral_angle_1_deg 7.159 r_scangle_other 7.072 r_mcangle_it 6.064 r_mcangle_other 6.062 r_scbond_it 4.547 r_scbond_other 4.546 r_mcbond_it 3.838 r_mcbond_other 3.834 r_angle_refined_deg 1.606 r_angle_other_deg 1.323 r_chiral_restr 0.077 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 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 2293 Nucleic Acid Atoms Solvent Atoms 160 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing