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Dark state 2.2 Angstrom crystal structure of cobalamin binding domain belonging to a light-dependent transcription regulator TtCarH obtained under anaerobic condition
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8C31
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 Condition B3 from Morpheus screen (Molecular Dimensions) (0.09 M halogens, 0.1 M buffer system 1 pH 6.5, 30% v/v precipitant mix 3
Crystal Properties Matthews coefficient Solvent content 2.43 49.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.73 α = 90 b = 69.39 β = 90 c = 204.14 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 100 PIXEL DECTRIS EIGER2 X 16M 2021-07-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9762 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.2 57.4 100 1 14 12.3 46947
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.24 100 0.7 1.4 13.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 8C31 2.2 57.39 44464 2414 99.95 0.18131 0.17903 0.1899 0.2232 0.2286 RANDOM 60.629
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] 2.57 0.6 -3.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.775 r_dihedral_angle_2_deg 8.582 r_long_range_B_refined 8.055 r_long_range_B_other 8.041 r_dihedral_angle_1_deg 6.359 r_scangle_other 6.16 r_mcangle_other 4.182 r_mcangle_it 4.181 r_scbond_it 4.112 r_scbond_other 4.112
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.775 r_dihedral_angle_2_deg 8.582 r_long_range_B_refined 8.055 r_long_range_B_other 8.041 r_dihedral_angle_1_deg 6.359 r_scangle_other 6.16 r_mcangle_other 4.182 r_mcangle_it 4.181 r_scbond_it 4.112 r_scbond_other 4.112 r_mcbond_it 3.012 r_mcbond_other 3.012 r_angle_refined_deg 1.855 r_angle_other_deg 0.5 r_chiral_restr 0.087 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_gen_planes_other 0.003 r_bond_other_d 0.002 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 5905 Nucleic Acid Atoms Solvent Atoms 387 Heterogen Atoms 437
Software Software Software Name Purpose REFMAC refinement DIALS data reduction DIALS data scaling PHASER phasing