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Structure of PDK1-S241A mutant kinase domain
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 2.2 M AMMONIUM SULPHATE, 0.1 M TRIS PH7.5, pH 7.50
Crystal Properties Matthews coefficient Solvent content 2.9 0.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 121.827 α = 90 b = 121.827 β = 90 c = 47.75 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 2003-02-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 ESRF ID14-1
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 1.95 25 90.5 0.08 14.2 4.3 28782 2
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 1.95 2.02 99.2 0.42 2.3 3
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 1.95 25 27210 588 94.4 0.186 0.185 0.1948 0.23 0.2294 RANDOM 26.49
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] 1.53 0.76 1.53 -2.29
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.663 r_scangle_it 4.033 r_scbond_it 2.508 r_mcangle_it 1.676 r_angle_refined_deg 1.512 r_mcbond_it 0.909 r_angle_other_deg 0.867 r_symmetry_vdw_refined 0.758 r_symmetry_vdw_other 0.335 r_symmetry_hbond_refined 0.284
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.663 r_scangle_it 4.033 r_scbond_it 2.508 r_mcangle_it 1.676 r_angle_refined_deg 1.512 r_mcbond_it 0.909 r_angle_other_deg 0.867 r_symmetry_vdw_refined 0.758 r_symmetry_vdw_other 0.335 r_symmetry_hbond_refined 0.284 r_nbd_other 0.252 r_nbd_refined 0.208 r_xyhbond_nbd_refined 0.148 r_chiral_restr 0.091 r_nbtor_other 0.084 r_bond_refined_d 0.014 r_gen_planes_refined 0.007 r_gen_planes_other 0.004 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 2301 Nucleic Acid Atoms Solvent Atoms 166 Heterogen Atoms 108
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling CNS phasing