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An intermediate light exposed 2.15 Angstrom crystal structure of H132A variant of cobalamin binding domain belonging to a light-dependent transcription regulator TtCarH obtained under anaerobic conditions
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8C35
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.8 293 0.1 M ammonium sulfate, 0.1 M sodium citrate pH 5.8, 16% w/v PEG 4000, 20% v/v glycerol
Crystal Properties Matthews coefficient Solvent content 2.34 47.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.821 α = 90 b = 69.683 β = 90 c = 201.809 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 2021-10-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9795 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 2.15 61.82 100 1 18.2 13.4 48484
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 2.15 2.19 100 0.8 1 13.7
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 8C35 2.15 59.18 45993 2415 99.99 0.19528 0.19348 0.2158 0.22967 0.2455 RANDOM 52.317
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] 3.43 -2.06 -1.36
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.825 r_long_range_B_refined 8.078 r_long_range_B_other 8.06 r_dihedral_angle_2_deg 7.706 r_dihedral_angle_1_deg 5.879 r_scangle_other 5.753 r_mcangle_it 3.725 r_mcangle_other 3.725 r_scbond_it 3.716 r_scbond_other 3.716
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.825 r_long_range_B_refined 8.078 r_long_range_B_other 8.06 r_dihedral_angle_2_deg 7.706 r_dihedral_angle_1_deg 5.879 r_scangle_other 5.753 r_mcangle_it 3.725 r_mcangle_other 3.725 r_scbond_it 3.716 r_scbond_other 3.716 r_mcbond_it 2.593 r_mcbond_other 2.593 r_angle_refined_deg 2.107 r_angle_other_deg 0.529 r_chiral_restr 0.179 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 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 5897 Nucleic Acid Atoms Solvent Atoms 341 Heterogen Atoms 364
Software Software Software Name Purpose REFMAC refinement xia2 data reduction DIALS data scaling PHASER phasing