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Crystal Structure of the PDK1 Pleckstrin Homology (PH) domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other Other PDK1PH INSP4 MODEL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.5 30 % PEG 5000 MME, 0.2 M AMMONIUM SULPHATE, 0.1 M MES [PH 6.5]
Crystal Properties Matthews coefficient Solvent content 2 37.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.69 α = 90 b = 65.276 β = 97.49 c = 101.123 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 IMAGE PLATE RIGAKU RAXIS4 MIRRORS 2003-06-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007
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 1.45 30 97.5 0.05 13.2 4.5 95063 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 1.45 1.5 80.1 0.4 2.7 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-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDK1PH INSP4 MODEL 1.45 30 94091 934 97.4 0.157 0.156 0.206 RANDOM 21.98
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] 0.24 0.38 -0.28 0.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.938 r_dihedral_angle_4_deg 15.073 r_dihedral_angle_3_deg 12.993 r_dihedral_angle_1_deg 6.697 r_scangle_it 4.983 r_scbond_it 3.817 r_mcangle_it 2.271 r_mcbond_it 1.963 r_angle_refined_deg 1.576 r_angle_other_deg 0.827
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.938 r_dihedral_angle_4_deg 15.073 r_dihedral_angle_3_deg 12.993 r_dihedral_angle_1_deg 6.697 r_scangle_it 4.983 r_scbond_it 3.817 r_mcangle_it 2.271 r_mcbond_it 1.963 r_angle_refined_deg 1.576 r_angle_other_deg 0.827 r_mcbond_other 0.724 r_symmetry_vdw_other 0.289 r_nbd_refined 0.221 r_nbd_other 0.202 r_symmetry_vdw_refined 0.192 r_nbtor_refined 0.186 r_xyhbond_nbd_refined 0.166 r_symmetry_hbond_refined 0.162 r_chiral_restr 0.108 r_nbtor_other 0.094 r_xyhbond_nbd_other 0.084 r_bond_refined_d 0.015 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_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 4797 Nucleic Acid Atoms Solvent Atoms 715 Heterogen Atoms 74
Software Software Software Name Purpose REFMAC refinement CrystalClear data reduction d*TREK data scaling AMoRE phasing