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Crystal Structure of Phosphatidylinositol 5-Phosphate 4-Kinase (PI5P4K2C) bound to an allosteric inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2GK9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 22% w/v Peg3350, 0.3 M Ammonium Tartrate, 100mM PCPT pH 7.5
Crystal Properties Matthews coefficient Solvent content 2.58 52.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.414 α = 90 b = 114.794 β = 95.51 c = 146.853 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 PILATUS 6M-F 2018-11-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97625 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.39 146.17 72.6 0.8387 4.7 3.7 36705
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.39 2.46 0.359
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 2GK9 2.39 146.17 34407 1799 56.4 0.2137 0.211 0.2127 0.2657 0.2637 RANDOM 57.761
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] -1.76 1.85 -0.15 1.52
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.164 r_dihedral_angle_3_deg 19.175 r_dihedral_angle_4_deg 18.995 r_dihedral_angle_1_deg 7.866 r_angle_refined_deg 1.6 r_angle_other_deg 1.237 r_chiral_restr 0.073 r_bond_refined_d 0.01 r_gen_planes_refined 0.007 r_gen_planes_other 0.003
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.164 r_dihedral_angle_3_deg 19.175 r_dihedral_angle_4_deg 18.995 r_dihedral_angle_1_deg 7.866 r_angle_refined_deg 1.6 r_angle_other_deg 1.237 r_chiral_restr 0.073 r_bond_refined_d 0.01 r_gen_planes_refined 0.007 r_gen_planes_other 0.003 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9748 Nucleic Acid Atoms Solvent Atoms 199 Heterogen Atoms 108
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction Aimless data scaling PHASER phasing