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Crystal Structure of Phosphatidylinositol 5-phosphate 4-kinase type-2 alpha (PI5P4Ka) bound to an inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2YBX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 24 % PEG smear low
0.04 M CaCl
0.04 M NaFormate
0.1 M Tris pH pH 8.0
Crystal Properties Matthews coefficient Solvent content 2.28 46.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.661 α = 90 b = 84.935 β = 90 c = 128.346 γ = 90
Symmetry Space Group C 2 2 21
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 6M-F 2019-04-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9795 Diamond I04
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 2.096 42.504 84.7 0.04 0.056 0.04 0.996 10.3 1.9 19434 38.071
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.16 19.6 0.532 0.753 0.532 0.766 1.4 1.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.096 42.504 19422 961 84.206 0.22 0.2165 0.2046 0.2819 0.2654 51.147
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] 0.964 -0.161 -0.803
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.912 r_dihedral_angle_3_deg 15.452 r_lrange_it 7.694 r_lrange_other 7.681 r_dihedral_angle_2_deg 7.462 r_dihedral_angle_1_deg 6.926 r_scangle_it 6.032 r_scangle_other 6.03 r_mcangle_it 4.848 r_mcangle_other 4.847
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.912 r_dihedral_angle_3_deg 15.452 r_lrange_it 7.694 r_lrange_other 7.681 r_dihedral_angle_2_deg 7.462 r_dihedral_angle_1_deg 6.926 r_scangle_it 6.032 r_scangle_other 6.03 r_mcangle_it 4.848 r_mcangle_other 4.847 r_scbond_it 4.052 r_scbond_other 4.051 r_mcbond_it 3.406 r_mcbond_other 3.406 r_angle_refined_deg 1.461 r_angle_other_deg 0.487 r_nbd_refined 0.218 r_symmetry_nbd_other 0.194 r_nbtor_refined 0.189 r_xyhbond_nbd_refined 0.188 r_symmetry_xyhbond_nbd_refined 0.15 r_nbd_other 0.134 r_symmetry_nbd_refined 0.094 r_symmetry_nbtor_other 0.082 r_chiral_restr 0.065 r_symmetry_xyhbond_nbd_other 0.04 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2420 Nucleic Acid Atoms Solvent Atoms 125 Heterogen Atoms 27
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling PHASER phasing