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Dark state 2.1 Angstrom crystal structure of H132A variant 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 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 2.47 50.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.924 α = 90 b = 69.97 β = 90 c = 204.555 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 2021-09-11 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) 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 2.1 54.21 100 1 11.2 13.5 54612
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 2.1 2.16 100 0.8 1.7 12.7
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 8C31 2.1 51.19 51809 2722 99.95 0.18763 0.18577 0.2198 0.22269 0.2479 RANDOM 42.991
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] 6.53 -3.65 -2.88
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.658 r_dihedral_angle_2_deg 8.261 r_long_range_B_refined 7.209 r_long_range_B_other 7.141 r_dihedral_angle_1_deg 5.752 r_scangle_other 4.511 r_scbond_it 2.892 r_scbond_other 2.891 r_mcangle_it 2.736 r_mcangle_other 2.735
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.658 r_dihedral_angle_2_deg 8.261 r_long_range_B_refined 7.209 r_long_range_B_other 7.141 r_dihedral_angle_1_deg 5.752 r_scangle_other 4.511 r_scbond_it 2.892 r_scbond_other 2.891 r_mcangle_it 2.736 r_mcangle_other 2.735 r_angle_refined_deg 1.912 r_mcbond_it 1.866 r_mcbond_other 1.864 r_angle_other_deg 0.489 r_chiral_restr 0.111 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 5811 Nucleic Acid Atoms Solvent Atoms 432 Heterogen Atoms 436
Software Software Software Name Purpose REFMAC refinement xia2 data reduction DIALS data scaling PHASER phasing