☰ Navigation Tabs
Sulfate-complex structure of a pyrophosphate-dependent kinase in the ribokinase family provides insight into the donor-binding mode
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 1.94 36.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.745 α = 90 b = 62.354 β = 103.97 c = 87.979 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 1.47 50 95.7 27.8 3.4 79847
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 1.47 1.5
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 1.47 50 75813 4017 95.58 0.19305 0.19243 0.201 0.20448 0.2151 RANDOM 17.497
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] -0.45 -0.63 -0.17 0.83
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.921 r_dihedral_angle_4_deg 13.764 r_dihedral_angle_3_deg 12.867 r_dihedral_angle_1_deg 6.414 r_long_range_B_refined 2.531 r_long_range_B_other 2.499 r_angle_refined_deg 1.695 r_angle_other_deg 0.993 r_scangle_other 0.854 r_mcangle_it 0.671
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.921 r_dihedral_angle_4_deg 13.764 r_dihedral_angle_3_deg 12.867 r_dihedral_angle_1_deg 6.414 r_long_range_B_refined 2.531 r_long_range_B_other 2.499 r_angle_refined_deg 1.695 r_angle_other_deg 0.993 r_scangle_other 0.854 r_mcangle_it 0.671 r_mcangle_other 0.671 r_scbond_it 0.557 r_scbond_other 0.556 r_mcbond_it 0.399 r_mcbond_other 0.399 r_chiral_restr 0.102 r_bond_refined_d 0.014 r_gen_planes_refined 0.009 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 4269 Nucleic Acid Atoms Solvent Atoms 258 Heterogen Atoms 44
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling MOLREP phasing Coot model building