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Structure of Ribokinase from Giardia lamblia
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1RKD MR-rosetta starting from hhpred hit 1rkd
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.75 289 Microlytic MCSG1 screen, condition A9: 200mM Magnesium chloride, 22.5% (w/V) PEG 3350, 100mM HEPES free acid / NaOH pH 6.75: GilaA.01141.a.AE1.PS38632 at 34.66mg/ml: tray: 315276a9, cryo: 15% EG in 2 steps: puck vdk2-4
Crystal Properties Matthews coefficient Solvent content 2.1 41.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.62 α = 90 b = 169.92 β = 98.36 c = 84.14 γ = 90
Symmetry Space Group P 1 21 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 CCD RIGAKU SATURN 944+ 2020-03-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E+ SUPERBRIGHT 1.5418
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 2.65 46.83 99.4 0.1 0.11 0.997 15.47 6.18 35700 43.921
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 2.65 2.72 97.7 0.529 0.588 0.814 3.05 5.298
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE MR-rosetta starting from hhpred hit 1rkd 2.65 46.83 1.35 35692 1954 99.4 0.1814 0.1789 0.1808 0.2239 0.2249 0 46.9772
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 21.727 f_angle_d 0.776 f_chiral_restr 0.051 f_bond_d 0.005 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9527 Nucleic Acid Atoms Solvent Atoms 169 Heterogen Atoms 12
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PDB_EXTRACT data extraction MR-Rosetta phasing Coot model building PHASER phasing