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Dark state 1.8 Angstrom crystal structure of cobalamin binding domain belonging to a light-dependent transcription regulator TtCarH obtained under aerobic condition
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5C8A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 294 Condition B3 from Morpheus screen (Molecular Diensions) (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 2.46 49.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.114 α = 90 b = 69.705 β = 90 c = 204.544 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 XE 16M 2021-03-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.976 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim 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 1.8 61.18 96.7 0.086 1 16.7 13.6 84476
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 1.8 1.83 0.8 1
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 5C8A 1.8 61.18 80019 4383 98.31 0.17236 0.17044 0.1801 0.20897 0.2143 RANDOM 42.085
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] 2.12 0.23 -2.36
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.942 r_long_range_B_refined 12.166 r_long_range_B_other 12.037 r_dihedral_angle_2_deg 9.273 r_dihedral_angle_1_deg 5.669 r_scangle_other 4.889 r_scbond_it 3.331 r_scbond_other 3.331 r_mcangle_it 3.09 r_mcangle_other 3.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.942 r_long_range_B_refined 12.166 r_long_range_B_other 12.037 r_dihedral_angle_2_deg 9.273 r_dihedral_angle_1_deg 5.669 r_scangle_other 4.889 r_scbond_it 3.331 r_scbond_other 3.331 r_mcangle_it 3.09 r_mcangle_other 3.09 r_mcbond_it 2.307 r_mcbond_other 2.298 r_angle_refined_deg 1.991 r_angle_other_deg 0.544 r_chiral_restr 0.138 r_bond_refined_d 0.011 r_gen_planes_refined 0.008 r_bond_other_d 0.005 r_gen_planes_other 0.003 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 5910 Nucleic Acid Atoms Solvent Atoms 490 Heterogen Atoms 479
Software Software Software Name Purpose REFMAC refinement DIALS data reduction DIALS data scaling PHASER phasing