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Crystal Structure of PI5P4KIIAlpha complex with BI-D1870
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2YBX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 295 0.2 M Lithium sulfate monohydrate, 0.1 M HEPES pH 7.5, 25% (w/v) Polyethylene glycol 3350
Crystal Properties Matthews coefficient Solvent content 3 59.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 136.28 α = 90 b = 136.28 β = 90 c = 95.444 γ = 120
Symmetry Space Group P 61 2 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 MARMOSAIC 325 mm CCD 2015-05-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U 1.181 SSRF BL17U
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.7 40 100 0.149 0.155 0.041 10.3 14.2 14898
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.7 2.8 100 0.713 0.739 0.194 0.91 14.2
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 (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2YBX 2.7 40 14142 722 99.89 0.1951 0.1926 0.2417 0.26 RANDOM 61.397
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] 0.78 0.39 0.78 -2.54
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.543 r_dihedral_angle_4_deg 22.498 r_dihedral_angle_3_deg 17.41 r_dihedral_angle_1_deg 5.754 r_angle_refined_deg 1.256 r_chiral_restr 0.088 r_bond_refined_d 0.008 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2366 Nucleic Acid Atoms Solvent Atoms 100 Heterogen Atoms 43
Software Software Software Name Purpose HKL-2000 data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction REFMAC phasing