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DUF4465 domain containing protein in complex with vitamin B12.
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 7.5 298.15 35% (poly acrylic acid sodium salt) 2100
0.1M HEPES (pH 7.5)
0.2M ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 2.26 45.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 113.72 α = 90 b = 113.72 β = 90 c = 162.593 γ = 120
Symmetry Space Group P 32 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 77.36 PIXEL DECTRIS EIGER X 9M 2024-11-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-1 0.9655 ESRF MASSIF-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim 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 1.8 84.379 92.1 0.131 0.147 0.091 0.907 9.3 12.8 96344
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.849 1.879 96.8 1.362 0.751 0.964 0.373 1 1.299
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 1.85 84.379 95844 4618 92.077 0.191 0.1896 0.1897 0.2132 0.214 28.324
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] -0.298 -0.149 -0.298 0.965
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 13.691 r_dihedral_angle_3_deg 9.906 r_dihedral_angle_2_deg 8.678 r_dihedral_angle_1_deg 7.596 r_lrange_it 5.792 r_lrange_other 5.528 r_scangle_it 3.038 r_scangle_other 3.038 r_mcangle_it 2.446 r_mcangle_other 2.445
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 13.691 r_dihedral_angle_3_deg 9.906 r_dihedral_angle_2_deg 8.678 r_dihedral_angle_1_deg 7.596 r_lrange_it 5.792 r_lrange_other 5.528 r_scangle_it 3.038 r_scangle_other 3.038 r_mcangle_it 2.446 r_mcangle_other 2.445 r_angle_refined_deg 2.198 r_scbond_it 2.071 r_scbond_other 2.071 r_mcbond_it 1.603 r_mcbond_other 1.603 r_angle_other_deg 0.837 r_nbd_refined 0.19 r_nbtor_refined 0.172 r_symmetry_xyhbond_nbd_refined 0.17 r_symmetry_nbd_other 0.16 r_nbd_other 0.156 r_xyhbond_nbd_refined 0.154 r_chiral_restr 0.094 r_symmetry_nbtor_other 0.078 r_metal_ion_refined 0.077 r_symmetry_nbd_refined 0.071 r_ncsr_local_group_3 0.066 r_ncsr_local_group_2 0.064 r_ncsr_local_group_1 0.057 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_gen_planes_other 0.004 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5126 Nucleic Acid Atoms Solvent Atoms 665 Heterogen Atoms 282
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing