☰ Navigation Tabs
Dark state 1.8 Angstrom crystal structure of cobalamin binding domain belonging to a light-dependent transcription regulator TtCarH obtained under aerobic condition form ll
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 BATCH MODE 7.5 293.15 PEG 10000 20%, 0.1 M HEPES pH 7.5
Crystal Properties Matthews coefficient Solvent content 2.8 56.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.519 α = 90 b = 66.501 β = 90 c = 205.245 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 EIGER X 16M 2022-04-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.8856 ESRF ID23-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.7 30 99.6 0.032 0.032 0.999 13.8 2 97589
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.7 1.76 99.5 0.493 0.697 0.569 1.3 2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 FREE R-VALUE 1.7 29.91 1.7 92941 4905 99.81 0.17289 0.17096 0.1732 0.21002 0.1718 RANDOM 34.007
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] -0.32 0.61 -0.29
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.453 r_dihedral_angle_2_deg 8.697 r_long_range_B_refined 8.139 r_dihedral_angle_1_deg 5.384 r_scbond_it 4.532 r_mcangle_it 3.887 r_mcbond_it 2.901 r_angle_refined_deg 2.079 r_chiral_restr 0.172 r_bond_refined_d 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.453 r_dihedral_angle_2_deg 8.697 r_long_range_B_refined 8.139 r_dihedral_angle_1_deg 5.384 r_scbond_it 4.532 r_mcangle_it 3.887 r_mcbond_it 2.901 r_angle_refined_deg 2.079 r_chiral_restr 0.172 r_bond_refined_d 0.01 r_gen_planes_refined 0.01 r_bond_other_d r_angle_other_deg r_dihedral_angle_4_deg r_gen_planes_other 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_mcbond_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5883 Nucleic Acid Atoms Solvent Atoms 914 Heterogen Atoms 436
Software Software Software Name Purpose REFMAC refinement XSCALE data scaling PHASER phasing Coot model building