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Crystal structure of CX-4945 bound Cka1 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, 5mM CX-4945
Crystal Properties Matthews coefficient Solvent content 2.61 52.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.762 α = 90 b = 95.395 β = 90 c = 94.518 γ = 90
Symmetry Space Group C 2 2 21
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 6M 2018-05-21 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) 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 2.09 65.79 97 0.02506 0.999 15.7 2 23770
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.094 2.169 0.2672 0.884
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 2.09 47.74 21739 1995 96.81 0.18936 0.18673 0.1932 0.2186 0.2275 RANDOM 36.927
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] -0.02 0.01 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.553 r_dihedral_angle_4_deg 22.358 r_dihedral_angle_3_deg 13.988 r_long_range_B_refined 8.172 r_long_range_B_other 8.171 r_scangle_other 6.097 r_dihedral_angle_1_deg 5.905 r_scbond_it 4.001 r_scbond_other 4.001 r_mcangle_it 3.871
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.553 r_dihedral_angle_4_deg 22.358 r_dihedral_angle_3_deg 13.988 r_long_range_B_refined 8.172 r_long_range_B_other 8.171 r_scangle_other 6.097 r_dihedral_angle_1_deg 5.905 r_scbond_it 4.001 r_scbond_other 4.001 r_mcangle_it 3.871 r_mcangle_other 3.87 r_mcbond_it 2.763 r_mcbond_other 2.763 r_angle_refined_deg 1.609 r_angle_other_deg 1.495 r_chiral_restr 0.088 r_bond_refined_d 0.011 r_gen_planes_refined 0.008 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 2739 Nucleic Acid Atoms Solvent Atoms 99 Heterogen Atoms 30
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing