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Pyrophosphate-dependent kinase in the ribokinase family complexed with a pyrophosphate analog and myo-inositol
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1VK4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.6 293 PEG 4000, ammonium sulfate, sodium acetate
Crystal Properties Matthews coefficient Solvent content 1.99 38.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.673 α = 90 b = 63.009 β = 105.05 c = 89.884 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 PIXEL DECTRIS PILATUS3 6M 2016-10-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1.000 SPring-8 BL41XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.7 50 98.1 24.8 3.3 54308
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.7 1.73
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 THROUGHOUT 1VK4 1.7 50 51566 2727 97.93 0.19713 0.19644 0.2035 0.21042 0.2189 RANDOM 33.113
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] -1.05 0.61 0.04 0.59
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.238 r_dihedral_angle_4_deg 13.499 r_dihedral_angle_3_deg 12.15 r_dihedral_angle_1_deg 5.986 r_long_range_B_refined 2.836 r_long_range_B_other 2.824 r_angle_refined_deg 1.382 r_scangle_other 0.941 r_angle_other_deg 0.913 r_mcangle_it 0.812
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.238 r_dihedral_angle_4_deg 13.499 r_dihedral_angle_3_deg 12.15 r_dihedral_angle_1_deg 5.986 r_long_range_B_refined 2.836 r_long_range_B_other 2.824 r_angle_refined_deg 1.382 r_scangle_other 0.941 r_angle_other_deg 0.913 r_mcangle_it 0.812 r_mcangle_other 0.812 r_scbond_it 0.591 r_scbond_other 0.588 r_mcbond_it 0.489 r_mcbond_other 0.489 r_chiral_restr 0.078 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4079 Nucleic Acid Atoms Solvent Atoms 95 Heterogen Atoms 39
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling MOLREP phasing Coot model building