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Crystal structure of human PDK2 complexed with GM67520
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 sulfate, 0.1M Bis-Tris pH 6.5, 25% Polyethylene glycol 3350
Crystal Properties Matthews coefficient Solvent content 2.37 48.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.949 α = 90 b = 95.122 β = 90 c = 162.503 γ = 90
Symmetry Space Group P 21 21 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 CCD ADSC QUANTUM 270 2019-03-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 7A (6B, 6C1) 0.9792 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 1.76 50 97.4 0.094 0.101 0.037 8 7.5 86058
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 1.76 1.79 99.8 1.734 1.889 0.736 0.55 6.4
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4MP2 1.76 36.53 76621 4055 91.32 0.236 0.2343 0.2688 0.2468 RANDOM 34.766
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] 0.01 1.31 -1.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.534 r_dihedral_angle_4_deg 20.781 r_dihedral_angle_3_deg 14.511 r_dihedral_angle_1_deg 6.377 r_angle_refined_deg 1.595 r_angle_other_deg 1.409 r_chiral_restr 0.083 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.534 r_dihedral_angle_4_deg 20.781 r_dihedral_angle_3_deg 14.511 r_dihedral_angle_1_deg 6.377 r_angle_refined_deg 1.595 r_angle_other_deg 1.409 r_chiral_restr 0.083 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5769 Nucleic Acid Atoms Solvent Atoms 451 Heterogen Atoms 126
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling PDB_EXTRACT data extraction HKL-2000 data reduction MOLREP phasing