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Crystal structure of P7C8 bound to CK2alpha
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5CVH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 293 0.2 M Ammonium sulfate, 30 % w/v PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.36 47.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.461 α = 90 b = 63.25 β = 108.44 c = 58.672 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 88 PIXEL DECTRIS EIGER2 X 16M 2021-12-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9795 Diamond I04
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 1.48 55.66 99.8 0.077 0.079 0.019 1 18 17.1 66333
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 1.48 1.56 99.3 4.027 4.154 1.01 0.409 16.6
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 5CVH 1.48 55.66 62522 3442 99.18 0.1809 0.1797 0.187 0.2037 0.2125 RANDOM 33.211
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] 1.2 0.04 0.06 -1.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.302 r_dihedral_angle_4_deg 17.253 r_dihedral_angle_3_deg 14.298 r_dihedral_angle_1_deg 6.94 r_angle_refined_deg 1.672 r_angle_other_deg 1.378 r_chiral_restr 0.087 r_bond_refined_d 0.012 r_gen_planes_refined 0.01 r_gen_planes_other 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.302 r_dihedral_angle_4_deg 17.253 r_dihedral_angle_3_deg 14.298 r_dihedral_angle_1_deg 6.94 r_angle_refined_deg 1.672 r_angle_other_deg 1.378 r_chiral_restr 0.087 r_bond_refined_d 0.012 r_gen_planes_refined 0.01 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2865 Nucleic Acid Atoms Solvent Atoms 289 Heterogen Atoms 49
Software Software Software Name Purpose XDS data reduction Aimless data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction