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Structure of human PDK1 kinase domain in complex with BIM-2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1H1W PDB ENTRY 1H1W
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 2.3 M AMMONIUM SULPHATE 0.1 M TRIS-HCL PH 8.25
Crystal Properties Matthews coefficient Solvent content 3 58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 121.947 α = 90 b = 121.947 β = 90 c = 48.071 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 100 CCD ADSC CCD 2003-02-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 ESRF ID14-2
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 1.9 30 99.9 0.076 10 3.7 44644
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) 1 1.9 1.97 99.8 0.592 2.7 3.5
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 1H1W 1.9 30 31794 669 99.8 0.235 0.234 0.2398 0.279 0.2819 RANDOM 18.42
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] 0.46 0.23 0.46 -0.69
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 7.434 r_scangle_it 3.539 r_scbond_it 2.268 r_angle_refined_deg 1.602 r_mcangle_it 1.473 r_angle_other_deg 0.871 r_mcbond_it 0.826 r_symmetry_hbond_refined 0.263 r_nbd_other 0.243 r_symmetry_vdw_refined 0.221
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 7.434 r_scangle_it 3.539 r_scbond_it 2.268 r_angle_refined_deg 1.602 r_mcangle_it 1.473 r_angle_other_deg 0.871 r_mcbond_it 0.826 r_symmetry_hbond_refined 0.263 r_nbd_other 0.243 r_symmetry_vdw_refined 0.221 r_symmetry_vdw_other 0.217 r_nbd_refined 0.211 r_xyhbond_nbd_refined 0.197 r_chiral_restr 0.094 r_nbtor_other 0.087 r_bond_refined_d 0.015 r_gen_planes_refined 0.008 r_gen_planes_other 0.005 r_bond_other_d 0.002 r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_nbtor_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2297 Nucleic Acid Atoms Solvent Atoms 194 Heterogen Atoms 77
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing