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Last common ancestor of HMPPK and PLK/HMPPK vitamin kinases
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4C5K
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293 Protein: 20 mM tris 7.8, 10 mM MgCl, 10 mM ADP, 1 mM AlCl3 and 30 mM NaF. Crystalization condition: 0.2 M Magnesium chloride hexahydrate, 0.1 M Tris pH 7.0 and 10% w/v PEG 8000
Crystal Properties Matthews coefficient Solvent content 2.52 51.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.644 α = 90 b = 65.644 β = 90 c = 243.726 γ = 120
Symmetry Space Group P 65 2 2
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 PILATUS 2M 2018-06-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON LNLS BEAMLINE W01B-MX2 1.45854 LNLS W01B-MX2
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 2 46.58 99.91 0.1453 0.1525 0.04585 0.998 13.52 10.9 22065 25.56
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.072 99.86 1.07 0.3518 0.793 2.06 10
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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 4C5K 2 46.58 1.34 22052 1065 99.93 0.2079 0.2075 0.2079 0.2152 0.2137 27.22
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 19.7855 f_angle_d 1.0173 f_chiral_restr 0.0614 f_bond_d 0.0067 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1583 Nucleic Acid Atoms Solvent Atoms 122 Heterogen Atoms 12
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling MOLREP phasing