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Structure of human PDK1 kinase domain in complex with UCN-01
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 2.1 M AMMONIUM SULPHATE, 0.1 M TRIS-HCL PH 8.5 + 0.25 UL COBALTOUS CHLORIDE HEXAHYDRATE
Crystal Properties Matthews coefficient Solvent content 3 58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 123.387 α = 90 b = 123.387 β = 90 c = 47.115 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 2003-04-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 ESRF ID14-4
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 2.5 25 100 0.167 4.5 4.8 14395 33.9
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 2.5 2.59 99.9 0.688 2.6 4.4
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 2.51 24.52 14384 589 99.9 0.19 0.19 0.1808 0.257 0.2484 RANDOM 29.4
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] 4.7 3.82 4.7 -9.4
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 22.8 c_scangle_it 3.26 c_mcangle_it 2.4 c_scbond_it 2.2 c_angle_deg 1.8 c_mcbond_it 1.41 c_improper_angle_d 0.94 c_bond_d 0.009 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 22.8 c_scangle_it 3.26 c_mcangle_it 2.4 c_scbond_it 2.2 c_angle_deg 1.8 c_mcbond_it 1.41 c_improper_angle_d 0.94 c_bond_d 0.009 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2216 Nucleic Acid Atoms Solvent Atoms 102 Heterogen Atoms 97
Software Software Software Name Purpose CNS refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing