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Structure of Csm6' from Streptococcus thermophilus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other D_1292126567 Strcuture of Csm6' in complex with cA6, split into 2 domains
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.95 M sodium citrate, 0.18 M sodium bromide and 0.1 M HEPES, pH 8
Crystal Properties Matthews coefficient Solvent content 3.91 68.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.646 α = 90 b = 104.138 β = 90 c = 144.478 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 77 PIXEL DECTRIS EIGER2 XE 16M 2019-10-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97901 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 3.54 29.52 95.2 0.09 1 9.4 3.8 15935
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.54 3.63 85.5 1.34 0.8 1.3 3.4
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3.54 29.52 15131 783 94.4 0.34359 0.34114 0.3381 0.38745 0.3886 RANDOM 41.071
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] -9.44 6.3 3.14
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 29.213 r_long_range_B_other 29.21 r_mcangle_it 21.518 r_mcangle_other 21.515 r_scangle_other 19.999 r_dihedral_angle_3_deg 19.326 r_mcbond_it 12.991 r_mcbond_other 12.99 r_scbond_it 11.875 r_scbond_other 11.861
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 29.213 r_long_range_B_other 29.21 r_mcangle_it 21.518 r_mcangle_other 21.515 r_scangle_other 19.999 r_dihedral_angle_3_deg 19.326 r_mcbond_it 12.991 r_mcbond_other 12.99 r_scbond_it 11.875 r_scbond_other 11.861 r_dihedral_angle_2_deg 9.728 r_dihedral_angle_1_deg 7.587 r_angle_refined_deg 0.226 r_angle_other_deg 0.094 r_chiral_restr 0.032 r_gen_planes_refined 0.011 r_gen_planes_other 0.002 r_bond_refined_d 0.001 r_bond_other_d r_dihedral_angle_4_deg 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 3168 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing