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Crystal structure of AMPPNP bound CK2 alpha from C. neoformans
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1LP4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 290 0.2 M lithium sulfate, 0.1 M Tris pH 8.5, 30 %(w/v) PEG 4000, 30%(w/v) dextran sulfate sodium salt, 2 mM MgCl2, 5 mM AMPPNP
Crystal Properties Matthews coefficient Solvent content 2.53 51.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.877 α = 90 b = 95.594 β = 90.04 c = 93.3 γ = 90
Symmetry Space Group C 1 2 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 PILATUS3 S 6M 2018-04-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 11C 0.97 PAL/PLS 11C
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 2.8 50 97.84 0.075 18.7 5.1 18151
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 2.8 2.85 0.161
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 1LP4 2.8 47.84 18151 928 97.84 0.19808 0.19639 0.1988 0.22974 0.2298 RANDOM 38.953
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 -0.02 -0.03 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.186 r_dihedral_angle_4_deg 19.747 r_dihedral_angle_3_deg 17.608 r_long_range_B_refined 9.311 r_long_range_B_other 9.31 r_dihedral_angle_1_deg 7.263 r_scangle_other 5.273 r_mcangle_it 4.402 r_mcangle_other 4.401 r_scbond_it 3.253
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.186 r_dihedral_angle_4_deg 19.747 r_dihedral_angle_3_deg 17.608 r_long_range_B_refined 9.311 r_long_range_B_other 9.31 r_dihedral_angle_1_deg 7.263 r_scangle_other 5.273 r_mcangle_it 4.402 r_mcangle_other 4.401 r_scbond_it 3.253 r_scbond_other 3.252 r_mcbond_it 2.651 r_mcbond_other 2.648 r_angle_other_deg 1.572 r_angle_refined_deg 1.556 r_chiral_restr 0.077 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5450 Nucleic Acid Atoms Solvent Atoms 8 Heterogen Atoms 86
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling REFMAC phasing