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Crystal structure of human PDK4-ADP complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1Y8N PDB entry 1Y8N
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 1.9M ammonium sulfate, 4% polyethylene glycol 400, 100mM potassium phosphate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.21 44.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.616 α = 90 b = 68.743 β = 100.1 c = 81.554 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 CCD ADSC QUANTUM 315 mirrrors 2008-02-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.98 APS 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 50 99.6 0.056 23.4 4.1 52354
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2 2.03 100 0.665 2.4 4.2 2631
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 PDB entry 1Y8N 2 49.22 49635 2668 99.37 0.18771 0.18488 0.2239 0.24016 0.275 RANDOM 41.96
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] -0.21 -0.2 1.08 -0.94
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.923 r_dihedral_angle_4_deg 21.24 r_dihedral_angle_3_deg 16.176 r_dihedral_angle_1_deg 5.851 r_scangle_it 4.52 r_scbond_it 3.165 r_mcangle_it 1.842 r_angle_refined_deg 1.831 r_mcbond_it 1.387 r_nbtor_refined 0.317
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.923 r_dihedral_angle_4_deg 21.24 r_dihedral_angle_3_deg 16.176 r_dihedral_angle_1_deg 5.851 r_scangle_it 4.52 r_scbond_it 3.165 r_mcangle_it 1.842 r_angle_refined_deg 1.831 r_mcbond_it 1.387 r_nbtor_refined 0.317 r_nbd_refined 0.225 r_symmetry_hbond_refined 0.224 r_symmetry_vdw_refined 0.163 r_xyhbond_nbd_refined 0.139 r_chiral_restr 0.135 r_bond_refined_d 0.021 r_gen_planes_refined 0.008 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5737 Nucleic Acid Atoms Solvent Atoms 224 Heterogen Atoms 66
Software Software Software Name Purpose REFMAC refinement HKL-3000 data collection HKL-3000 data reduction HKL-3000 data scaling PHASER phasing