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B12-binding domain from Chloracidobacterium thermophilum MerR family protein, anaerobic light 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 Tris pH 8.5, 20% v/v Ethanol
Crystal Properties Matthews coefficient Solvent content 2.23 44.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 123.485 α = 90 b = 123.485 β = 90 c = 73.105 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 2022-01-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9763 Diamond I03
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 2.299 106.941 100 0.2803 0.287 1 8.08 20.6 28905
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 2.3 2.34 99.9 2.463 2.75 0.5 0.72 19.7
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 2.3 106.94 27458 1426 99.99 0.20733 0.20636 0.2073 0.22527 0.2273 RANDOM 45.694
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] -0.17 -0.08 -0.17 0.55
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.498 r_dihedral_angle_2_deg 7.837 r_long_range_B_other 7.223 r_long_range_B_refined 7.222 r_dihedral_angle_1_deg 7.043 r_scangle_other 5.791 r_mcangle_it 4.208 r_mcangle_other 4.207 r_scbond_it 3.939 r_scbond_other 3.938
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.498 r_dihedral_angle_2_deg 7.837 r_long_range_B_other 7.223 r_long_range_B_refined 7.222 r_dihedral_angle_1_deg 7.043 r_scangle_other 5.791 r_mcangle_it 4.208 r_mcangle_other 4.207 r_scbond_it 3.939 r_scbond_other 3.938 r_mcbond_it 2.933 r_mcbond_other 2.901 r_angle_refined_deg 0.929 r_angle_other_deg 0.375 r_chiral_restr 0.043 r_bond_refined_d 0.005 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3591 Nucleic Acid Atoms Solvent Atoms 66 Heterogen Atoms 236
Software Software Software Name Purpose REFMAC refinement DIALS data reduction XSCALE data scaling PHASER phasing