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Crystal structures of human p70S6K1 kinase domain (Zinc anomalous)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3A62
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 289 2.5M sodium formate, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.61 52.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.408 α = 90 b = 69.408 β = 90 c = 143.378 γ = 90
Symmetry Space Group P 41 21 2
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 CCD ADSC unsupported-q315 2012-05-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U 1.2826 SSRF BL17U
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 2.1 50 96.3 0.121 12.2 8.9 20480
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 2.1 2.18 100 0.43 9.4 2073
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 3A62 2.1 46.48 20329 1033 95.78 0.2085 0.2065 0.2094 0.2467 0.2103 RANDOM 56.1127
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] -0.71 -0.71 1.42
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.264 r_dihedral_angle_4_deg 22.223 r_sphericity_bonded 19.468 r_dihedral_angle_3_deg 16.826 r_rigid_bond_restr 9.326 r_dihedral_angle_1_deg 5.126 r_angle_refined_deg 1.236 r_chiral_restr 0.085 r_bond_refined_d 0.009 r_gen_planes_refined 0.009
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.264 r_dihedral_angle_4_deg 22.223 r_sphericity_bonded 19.468 r_dihedral_angle_3_deg 16.826 r_rigid_bond_restr 9.326 r_dihedral_angle_1_deg 5.126 r_angle_refined_deg 1.236 r_chiral_restr 0.085 r_bond_refined_d 0.009 r_gen_planes_refined 0.009 r_sphericity_free
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2305 Nucleic Acid Atoms Solvent Atoms 61 Heterogen Atoms 29
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection