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A tetrapyrrole binding domain variant of CoaR in closed conformation at 2.28 angstrom resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.6 289 Bis-Tris, (NH4)2SO4, PEG3350
Crystal Properties Matthews coefficient Solvent content 4.24 73.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.043 α = 90 b = 96.043 β = 90 c = 148.664 γ = 120
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 EIGER2 S 9M 2024-06-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL02U1 0.9788 SSRF BL02U1
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 2.28 49.57 100 0.095 1 20.5 20.1 35426 48.17
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 2.28 2.34 100 1.755 0.791 2.3
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 2.28 45.74 33586 1733 99.79 0.20987 0.20884 0.2148 0.22974 0.2321 RANDOM 51.452
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] 0.2 0.1 0.2 -0.64
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.528 r_long_range_B_other 10.189 r_long_range_B_refined 10.181 r_scangle_other 7.464 r_mcangle_it 6.246 r_mcangle_other 6.245 r_dihedral_angle_1_deg 5.807 r_dihedral_angle_2_deg 4.811 r_scbond_it 4.805 r_scbond_other 4.535
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.528 r_long_range_B_other 10.189 r_long_range_B_refined 10.181 r_scangle_other 7.464 r_mcangle_it 6.246 r_mcangle_other 6.245 r_dihedral_angle_1_deg 5.807 r_dihedral_angle_2_deg 4.811 r_scbond_it 4.805 r_scbond_other 4.535 r_mcbond_it 4.073 r_mcbond_other 4.071 r_angle_refined_deg 1.27 r_angle_other_deg 0.461 r_chiral_restr 0.065 r_bond_refined_d 0.005 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 2943 Nucleic Acid Atoms Solvent Atoms 108 Heterogen Atoms 40
Software Software Software Name Purpose REFMAC refinement xia2 data reduction DIALS data scaling PHASER phasing