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Crystal structure of phosphatidyl inositol 4-kinase II beta in complex with MM1373
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4WTV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 10% w/v PEG 8.000, 20% v/v ethylene glycol, 3% v/v DMSO,
100 mM bicine/Trizma base pH 8.5,
20 mM 1,6-hexanediol, 20 mM 1-butanol, 20 mM 1,2-propanediol, 20 mM 2-propanol, 20 mM 1,4-butanediol, 20 mM 1,3-propanediol
Crystal Properties Matthews coefficient Solvent content 2.41 48.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.383 α = 90 b = 87.007 β = 107.78 c = 71.376 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 200K 2022-06-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.54187
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 2.4 31.63 92.17 0.09953 0.1164 0.05996 0.996 13.38 3.6 20410 32.31
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 2.4 2.486 84.38 0.6079 0.7059 0.3578 0.764 2.29 3.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 FREE R-VALUE 4WTV 2.4 31.63 1.34 20402 1020 92.23 0.2115 0.2105 0.2125 0.231 0.2328 random selection 43.98
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 10.8776 f_angle_d 0.477 f_chiral_restr 0.0402 f_plane_restr 0.0039 f_bond_d 0.0022
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3781 Nucleic Acid Atoms Solvent Atoms 106 Heterogen Atoms 22
Software Software Software Name Purpose XDS data reduction XDS data scaling PHASER phasing Coot model building PHENIX refinement