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Crystal structure of the tetrapyrrole binding domain in CoaR
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 289 (NH4)2SO4, Tris, PEG 8000
Crystal Properties Matthews coefficient Solvent content 2.51 50.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 94.365 α = 90 b = 101.5 β = 90 c = 48.653 γ = 90
Symmetry Space Group P 21 21 2
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 0.97881 SSRF BL02U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 2.26 34.58 98.4 0.104 0.11 0.035 0.995 15.9 9.6 22245 29.59
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.26 2.34 87.1 0.83 0.997 0.533 0.22 3.5 3.5
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 2.26 34.56 22197 1076 98.009 0.193 0.1921 0.2006 0.2097 0.2127 34.602
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] 1.195 -2.278 1.084
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 13.522 r_dihedral_angle_3_deg 12.582 r_lrange_it 6.15 r_lrange_other 6.077 r_dihedral_angle_1_deg 5.868 r_dihedral_angle_2_deg 4.946 r_scangle_it 4.124 r_scangle_other 4.123 r_mcangle_it 3.204 r_mcangle_other 3.203
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 13.522 r_dihedral_angle_3_deg 12.582 r_lrange_it 6.15 r_lrange_other 6.077 r_dihedral_angle_1_deg 5.868 r_dihedral_angle_2_deg 4.946 r_scangle_it 4.124 r_scangle_other 4.123 r_mcangle_it 3.204 r_mcangle_other 3.203 r_scbond_it 2.336 r_scbond_other 2.336 r_mcbond_it 1.882 r_mcbond_other 1.881 r_angle_refined_deg 1.114 r_angle_other_deg 0.396 r_nbd_other 0.2 r_nbd_refined 0.187 r_symmetry_nbd_other 0.183 r_nbtor_refined 0.157 r_symmetry_nbd_refined 0.131 r_xyhbond_nbd_refined 0.128 r_symmetry_xyhbond_nbd_refined 0.11 r_symmetry_nbtor_other 0.074 r_chiral_restr 0.053 r_bond_refined_d 0.003 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2639 Nucleic Acid Atoms Solvent Atoms 119 Heterogen Atoms 12
Software Software Software Name Purpose REFMAC refinement xia2 data reduction DIALS data scaling PHASER phasing