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Crystal structure of P8C9 bound to CK2alpha
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5CU6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.2 298 12 %v/v PEGSH, 0.1 M Mg Acet,
0.1 M KCl,0.1 M MES
Crystal Properties Matthews coefficient Solvent content 2.12 42.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.374 α = 90 b = 65.019 β = 111.2 c = 59.198 γ = 90
Symmetry Space Group P 1 21 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 PIXEL DECTRIS EIGER2 XE 16M 2019-09-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9762 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.19 55.19 91.9 0.11 0.114 0.029 0.999 12.9 14.5 116431
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 1.19 1.26 56.4 2.478 2.649 0.908 0.341 8.2
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5CU6 1.19 55.19 110272 5925 91.67 0.1729 0.1719 0.1817 0.1899 0.198 RANDOM 20.316
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] -0.01 0.09 -0.7 0.49
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.077 r_dihedral_angle_4_deg 19.716 r_dihedral_angle_3_deg 14.06 r_dihedral_angle_1_deg 6.891 r_angle_refined_deg 1.812 r_angle_other_deg 1.476 r_chiral_restr 0.102 r_bond_refined_d 0.014 r_gen_planes_refined 0.011 r_gen_planes_other 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.077 r_dihedral_angle_4_deg 19.716 r_dihedral_angle_3_deg 14.06 r_dihedral_angle_1_deg 6.891 r_angle_refined_deg 1.812 r_angle_other_deg 1.476 r_chiral_restr 0.102 r_bond_refined_d 0.014 r_gen_planes_refined 0.011 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2958 Nucleic Acid Atoms Solvent Atoms 354 Heterogen Atoms 36
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing PDB_EXTRACT data extraction