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B12-binding domain from Chloracidobacterium thermophilum MerR family protein, dark state
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 277 0.1M Amino acids, 0.1 M Buffer System 3 (Bicine and Tris) pH 8.5, 50% v/v Precipitant Mix 3 (Glycerol and Poly(ethylene glycol) 4000)
Crystal Properties Matthews coefficient Solvent content 2.29 46.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 125.218 α = 90 b = 125.218 β = 90 c = 73.088 γ = 120
Symmetry Space Group P 31 2 1
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 2021-11-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9762 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 2.3 108.442 100 0.163 1 12.5 20.6 29650
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.34 98.91 2.659 0.538 0.62 19.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.3 108.44 28126 1503 99.92 0.18791 0.18531 0.1981 0.23609 0.2427 RANDOM 59.044
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] -2.25 -1.12 -2.25 7.29
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.45 r_long_range_B_other 9.876 r_long_range_B_refined 9.874 r_dihedral_angle_2_deg 9.541 r_scangle_other 8.293 r_mcangle_it 6.933 r_mcangle_other 6.933 r_dihedral_angle_1_deg 6.659 r_scbond_it 5.79 r_scbond_other 5.789
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.45 r_long_range_B_other 9.876 r_long_range_B_refined 9.874 r_dihedral_angle_2_deg 9.541 r_scangle_other 8.293 r_mcangle_it 6.933 r_mcangle_other 6.933 r_dihedral_angle_1_deg 6.659 r_scbond_it 5.79 r_scbond_other 5.789 r_mcbond_it 5.055 r_mcbond_other 5.044 r_angle_refined_deg 2.021 r_angle_other_deg 0.609 r_chiral_restr 0.092 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_gen_planes_other 0.002 r_bond_other_d 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 3788 Nucleic Acid Atoms Solvent Atoms 37 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement DIALS data reduction XSCALE data scaling PHASER phasing