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Dual-specificity tyrosine phosphorylation-regulated kinase 1A in complex with coumestrol
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5A3X
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7 291 20% Jeffamine ED-200, 0.1 M Imidazole
Crystal Properties Matthews coefficient Solvent content 2.77 55.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 132.689 α = 90 b = 132.689 β = 90 c = 91.465 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 95 CCD RAYONIX MX300-HS 2020-12-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE TPS 05A 1.0 NSRRC TPS 05A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.25 25 100 0.91 42.2 12.5 43425 28.4162210137
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.25 2.33 0.91
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.25152331476 24.326528802 1.35614394759 43401 2225 99.9700557424 0.187271484388 0.18450364397 0.1842 0.23851980932 0.2379 33.6909353426
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 6.96634617663 f_angle_d 0.947162575849 f_chiral_restr 0.0546174056427 f_bond_d 0.00827327535292 f_plane_restr 0.00619994829728
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5627 Nucleic Acid Atoms Solvent Atoms 434 Heterogen Atoms 40
Software Software Software Name Purpose PHENIX refinement HKL-3000 data reduction HKL-3000 data scaling MOLREP phasing