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B12 Binding protein - BtuK1
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 6.5 294.15 2mM Lanthanides, 0.1M Buffer systems 4 (MOPSO, Bis-Tris) (pH 6.5), 32.5% v/v Precipitant Mix 6 (25% w/v PEG 4000, 40% w/v 1,2,6 Hexanetriol)
Crystal Properties Matthews coefficient Solvent content 2.51 50.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.739 α = 90 b = 129.984 β = 90 c = 164.66 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 9M 2025-07-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID30B 0.87313 ESRF ID30B
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 1.65 46.85 96.2 1 11.4 1 131196
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 1.65 1.71 0.5
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.817 14.287 99154 4991 96.307 0.164 0.1625 0.1643 0.1917 0.1954 34.173
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] 0.527 -0.598 0.071
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.9 r_dihedral_angle_other_2_deg 12.241 r_dihedral_angle_3_deg 11.669 r_dihedral_angle_1_deg 8.362 r_dihedral_angle_2_deg 8.173 r_lrange_it 5.779 r_lrange_other 5.638 r_scangle_it 3.933 r_scangle_other 3.932 r_scbond_it 2.536
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.9 r_dihedral_angle_other_2_deg 12.241 r_dihedral_angle_3_deg 11.669 r_dihedral_angle_1_deg 8.362 r_dihedral_angle_2_deg 8.173 r_lrange_it 5.779 r_lrange_other 5.638 r_scangle_it 3.933 r_scangle_other 3.932 r_scbond_it 2.536 r_scbond_other 2.534 r_angle_refined_deg 2.15 r_mcangle_it 2.107 r_mcangle_other 2.107 r_mcbond_it 1.552 r_mcbond_other 1.55 r_angle_other_deg 1.386 r_nbtor_refined 0.15 r_nbd_refined 0.138 r_chiral_restr 0.123 r_symmetry_nbd_refined 0.114 r_symmetry_nbd_other 0.112 r_nbd_other 0.112 r_symmetry_xyhbond_nbd_refined 0.111 r_xyhbond_nbd_refined 0.109 r_ncsr_local_group_1 0.083 r_ncsr_local_group_3 0.08 r_ncsr_local_group_2 0.077 r_symmetry_nbtor_other 0.058 r_gen_planes_refined 0.014 r_bond_refined_d 0.012 r_bond_other_d 0.009 r_gen_planes_other 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7939 Nucleic Acid Atoms Solvent Atoms 642 Heterogen Atoms 279
Software Software Software Name Purpose Aimless data scaling gemmi data extraction REFMAC refinement autoPROC data reduction PHASER phasing