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Structure of human PDK1 kinase domain in complex with staurosporine
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 7.2
Crystal Properties Matthews coefficient Solvent content 3 58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 124.172 α = 90 b = 124.172 β = 90 c = 47.314 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 2002-07-15 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 2.3 25 95.8 0.096 7.5 1.8 18018 28.1
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 2.3 2.38 95.8 0.505 1.8 1.7
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 2.3 24.67 18012 753 95.7 0.219 0.219 0.2069 0.255 0.2402 RANDOM 33.1
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] 4.52 2.01 4.52 -9.05
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 22 c_scangle_it 3.22 c_mcangle_it 2.58 c_scbond_it 2.15 c_angle_deg 1.7 c_mcbond_it 1.54 c_improper_angle_d 0.77 c_bond_d 0.007 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 22 c_scangle_it 3.22 c_mcangle_it 2.58 c_scbond_it 2.15 c_angle_deg 1.7 c_mcbond_it 1.54 c_improper_angle_d 0.77 c_bond_d 0.007 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 2288 Nucleic Acid Atoms Solvent Atoms 97 Heterogen Atoms 78
Software Software Software Name Purpose CNS refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing