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Anaerobic light exposed 2.25 Angstrom crystal structure of cobalamin binding domain belonging to a light-dependent transcription regulator TtCarH
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
dark adapted crystals were exposed to light under anaerobic conditions inside a glove box for 30-40 secs
Crystal Properties Matthews coefficient Solvent content 2.39 48.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.918 α = 90 b = 72.622 β = 90 c = 200.943 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 2021-10-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9765 Diamond I04
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 2.25 60.92 100 1 9.4 13.4 43294
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 2.25 2.29 98.4 0.7 1.2 13.3
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 2.25 58.93 41071 2147 99.91 0.20009 0.19758 0.2039 0.24798 0.2553 RANDOM 39.485
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] 0.25 -1.83 1.59
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.14 r_dihedral_angle_2_deg 8.069 r_dihedral_angle_1_deg 5.737 r_long_range_B_refined 5.586 r_long_range_B_other 5.562 r_scangle_other 4.105 r_mcangle_it 2.688 r_mcangle_other 2.688 r_scbond_it 2.527 r_scbond_other 2.526
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.14 r_dihedral_angle_2_deg 8.069 r_dihedral_angle_1_deg 5.737 r_long_range_B_refined 5.586 r_long_range_B_other 5.562 r_scangle_other 4.105 r_mcangle_it 2.688 r_mcangle_other 2.688 r_scbond_it 2.527 r_scbond_other 2.526 r_angle_refined_deg 1.867 r_mcbond_it 1.736 r_mcbond_other 1.736 r_angle_other_deg 0.488 r_chiral_restr 0.079 r_bond_refined_d 0.009 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 6003 Nucleic Acid Atoms Solvent Atoms 334 Heterogen Atoms 365
Software Software Software Name Purpose REFMAC refinement DIALS data reduction DIALS data scaling PHASER phasing