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LOW-SALT STRUCTURE OF PROTEIN KINASE CK2 CATALYTIC SUBUNIT (ISOFORM CK2ALPHA) IN COMPLEX WITH THE INDENOINDOLE-TYPE INHIBITOR 4P
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2PVR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 90 MICROLITER ENZYME STOCK SOLUTION (6 MG/ML IN 500 MM NACL, 25 MM
TRIS/HCL, PH 8.5) WAS MIXED WITH 10 MIKROLITER 4P STOCK
SOLUTION (10 MM 4P IN DMSO). THIS MIXTURE WAS INCUBATED FOR 30
MIN AT ROOM TEMPERATURE. THE RESERVOIR SOLUTION OF THE
CRYSTALLIZATION EXPERIMENT WAS 25 % (W/V) PEG5000, 0.2 M
AMMONIUM SULPHATE, 0.1 M MES BUFFER, PH 6.5. PRIOR TO
EQUILIBRATION THE CRYSTALLIZATION DROP WAS COMPOSED OF 1
MICROLITER RESERVOIR SOLUTION PLUS 1 MICROLITER ENZYME/4P
MIXTURE., VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K
Crystal Properties Matthews coefficient Solvent content 3.2 61.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 128.453 α = 90 b = 128.453 β = 90 c = 124.106 γ = 90
Symmetry Space Group P 43 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 PIXEL DECTRIS PILATUS 2M 2016-12-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-1 0.9660 ESRF MASSIF-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) CC (Half) 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 57.041 99.51 0.06473 0.06473 0.999 14.2 6.2 70221 44.4
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.072 98.84 1.909 1.909 0.437 0.93 6.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2PVR 2 57.041 1.97 70115 1388 99.52 0.1757 0.1751 0.2042 0.2138
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 13.195 f_angle_d 0.807 f_chiral_restr 0.054 f_bond_d 0.007 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5634 Nucleic Acid Atoms Solvent Atoms 297 Heterogen Atoms 113
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing