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Crystal structure of human PDK2 complexed with an allosteric inhibitor compound 8c
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4MP2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.2M Ammonium citrate tribasic pH 7.0, 20% w/v Polyethylene glycol 3,350
Crystal Properties Matthews coefficient Solvent content 2.36 47.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.778 α = 88.2 b = 52.839 β = 78 c = 92.145 γ = 60.93
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 270 2019-05-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 7A (6B, 6C1) 0.9793 PAL/PLS 7A (6B, 6C1)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.93 50 97.5 0.104 0.122 0.063 9.9 3.7 62684
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 1.93 1.96 96.3 1.231 1.437 0.738 0.682 3.7
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 4MP2 1.93 29.8 59243 2955 97.47 0.1933 0.1913 0.1991 0.2314 0.2327 RANDOM 37.285
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] -0.9 -1.43 0.97 -0.36 -0.72 0.67
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.306 r_dihedral_angle_4_deg 20.787 r_dihedral_angle_3_deg 14.966 r_dihedral_angle_1_deg 6.481 r_angle_refined_deg 1.528 r_angle_other_deg 1.351 r_chiral_restr 0.079 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.306 r_dihedral_angle_4_deg 20.787 r_dihedral_angle_3_deg 14.966 r_dihedral_angle_1_deg 6.481 r_angle_refined_deg 1.528 r_angle_other_deg 1.351 r_chiral_restr 0.079 r_bond_refined_d 0.009 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 5438 Nucleic Acid Atoms Solvent Atoms 246 Heterogen Atoms 112
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling PDB_EXTRACT data extraction HKL-2000 data reduction MOLREP phasing