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Crystal structure of the ribokinase RBK1 in complex with ribose from Saccharomyces cerevisiae
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 291 0.2M Sodium formate, 0.1M Bicine pH 8.6, 24% PEG 5000, 0.04% 1,2-Diaminocyclohexane sulfate, 0.04% Diloxanide furoate, 0.04% Fumaric acid, 0.04% Spermine, 0.04% Sulfaguanidine, 0.004M HEPES sodium pH 6.8
Crystal Properties Matthews coefficient Solvent content 2.72 54.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.84 α = 90 b = 169.06 β = 90 c = 117.87 γ = 90
Symmetry Space Group C 2 2 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 16M 2023-09-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL10U2 0.978797 SSRF BL10U2
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 2.91 84.53 99.2 0.997 14.3 12.3 17881
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 2.91 2.99 0.557
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.91 36.47 1.34 17881 890 98.8 0.2426 0.2402 0.2413 0.2935 0.2947
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 7.771 f_angle_d 0.864 f_chiral_restr 0.051 f_plane_restr 0.009 f_bond_d 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4649 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 20
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHENIX phasing