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PDK-1 in complex with the inhibitor Compound-8i
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.88 57.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 122.874 α = 90 b = 122.874 β = 90 c = 47.16 γ = 120
Symmetry Space Group P 32 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 93 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E SUPERBRIGHT
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.2 100 19841
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 (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 2.2 23.17 19841 1076 99.42 0.24004 0.23807 0.2374 0.2777 0.2779 RANDOM 26.276
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] 0.63 0.31 0.63 -0.94
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.665 r_dihedral_angle_4_deg 17.753 r_dihedral_angle_3_deg 14.36 r_dihedral_angle_1_deg 4.945 r_scangle_it 1.197 r_angle_refined_deg 0.964 r_scbond_it 0.715 r_mcangle_it 0.711 r_mcbond_it 0.406 r_nbtor_refined 0.304
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.665 r_dihedral_angle_4_deg 17.753 r_dihedral_angle_3_deg 14.36 r_dihedral_angle_1_deg 4.945 r_scangle_it 1.197 r_angle_refined_deg 0.964 r_scbond_it 0.715 r_mcangle_it 0.711 r_mcbond_it 0.406 r_nbtor_refined 0.304 r_nbd_refined 0.173 r_symmetry_vdw_refined 0.146 r_symmetry_hbond_refined 0.122 r_xyhbond_nbd_refined 0.105 r_chiral_restr 0.07 r_bond_refined_d 0.007 r_gen_planes_refined 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2260 Nucleic Acid Atoms Solvent Atoms 86 Heterogen Atoms 36
Software Software Software Name Purpose HKL-2000 data collection AMoRE phasing REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling