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Crystal structure of adenosylcobinamide kinase / adenosylcobinamide phosphate guanylyltransferase complexed with adenosylcobinamide-phosphate
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 293 0.15 M Sodium Chloride, 0.1 M Bis-Tris: HCl, pH 6.5, 1.3 M Ammonium Sulfate
Crystal Properties Matthews coefficient Solvent content 2.85 56.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 99.213 α = 90 b = 102.922 β = 90 c = 129.228 γ = 90
Symmetry Space Group P 2 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 2023-03-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 5C (4A) 0.97942 PAL/PLS 5C (4A)
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 2.6 47.964 99.9 1 15.4 6.4 41344
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 2.6 2.71 1
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 2.6 47.964 41304 2119 99.761 0.197 0.1931 0.1972 0.2633 0.2645 66.423
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] -0.002 -0.013 0.015
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.493 r_dihedral_angle_3_deg 19.774 r_dihedral_angle_4_deg 17.102 r_lrange_it 13.676 r_lrange_other 13.675 r_scangle_it 9.386 r_scangle_other 9.37 r_mcangle_it 8.145 r_mcangle_other 8.145 r_dihedral_angle_1_deg 7.824
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.493 r_dihedral_angle_3_deg 19.774 r_dihedral_angle_4_deg 17.102 r_lrange_it 13.676 r_lrange_other 13.675 r_scangle_it 9.386 r_scangle_other 9.37 r_mcangle_it 8.145 r_mcangle_other 8.145 r_dihedral_angle_1_deg 7.824 r_scbond_it 6.396 r_scbond_other 6.366 r_mcbond_it 5.646 r_mcbond_other 5.641 r_angle_refined_deg 2.18 r_angle_other_deg 1.223 r_nbd_other 0.225 r_nbd_refined 0.203 r_symmetry_nbd_other 0.196 r_symmetry_nbd_refined 0.179 r_nbtor_refined 0.153 r_xyhbond_nbd_refined 0.134 r_symmetry_xyhbond_nbd_refined 0.13 r_chiral_restr 0.111 r_symmetry_nbtor_other 0.086 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_gen_planes_other 0.003 r_symmetry_xyhbond_nbd_other 0.003 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8116 Nucleic Acid Atoms Solvent Atoms 27 Heterogen Atoms 610
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing