☰ Navigation Tabs
Conversion of pyrophosphate-dependent myo-inositol-1 kinase into myo-inositol-3 kinase by N78L/S89L mutation
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5YSP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 293 26% (w/v) poly(ethylene glycol) 4000, 2mM ammonium sulfate, 100mM sodium acetate buffer (pH 5.4)
Crystal Properties Matthews coefficient Solvent content 2.03 39.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.205 α = 83.53 b = 46.398 β = 80.43 c = 66.544 γ = 68.57
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 95 PIXEL DECTRIS PILATUS 2M 2019-11-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NE3A 1 Photon Factory AR-NE3A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.6 50 62.5 0.051 0.997 19.8 3.4 43707
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.6 1.64 94.6 0.134 0.985 9.1 3.58
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 FOURIER SYNTHESIS THROUGHOUT 5ysp 1.6 42.65 41534 2173 65.36 0.19301 0.19179 0.2002 0.21555 0.2225 RANDOM 15.558
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] -0.27 0.21 0.15 -0.33 0.32 0.87
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.024 r_dihedral_angle_4_deg 11.99 r_dihedral_angle_3_deg 11.658 r_dihedral_angle_1_deg 6.864 r_long_range_B_refined 3.233 r_long_range_B_other 3.218 r_angle_other_deg 2.307 r_scangle_other 1.689 r_mcangle_it 1.513 r_mcangle_other 1.513
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.024 r_dihedral_angle_4_deg 11.99 r_dihedral_angle_3_deg 11.658 r_dihedral_angle_1_deg 6.864 r_long_range_B_refined 3.233 r_long_range_B_other 3.218 r_angle_other_deg 2.307 r_scangle_other 1.689 r_mcangle_it 1.513 r_mcangle_other 1.513 r_angle_refined_deg 1.304 r_scbond_other 1.048 r_scbond_it 1.047 r_mcbond_it 0.894 r_mcbond_other 0.893 r_chiral_restr 0.057 r_bond_other_d 0.036 r_gen_planes_other 0.007 r_bond_refined_d 0.005 r_gen_planes_refined 0.005 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 4266 Nucleic Acid Atoms Solvent Atoms 193 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling REFMAC phasing