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Amicoumacin kinase AmiN in complex with AMP-PNP, Mg2+ and Ami
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 292 100 mM Tris-HCl, pH 8.5, 1.1 M LiCl, 27.5 % (w/v) PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.22 44.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.34 α = 89.95 b = 76.77 β = 99.62 c = 101.2 γ = 91.44
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 EIGER X 16M CRLs 2019-05-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2) 0.976 PETRA III, EMBL c/o DESY P14 (MX2)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 1.35 101.2 98.7 0.085 0.093 0.996 10.45 6.38 295613 19.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.35 1.39 96.9 1.39 1.57 0.506 1.9 4.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.35 99.78 277759 14034 98.71 0.151 0.1492 0.1503 0.1876 0.1888 RANDOM 27.089
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 -0.42 0.72 -0.04 -0.4 -1.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.619 r_sphericity_free 21.536 r_dihedral_angle_4_deg 21.452 r_dihedral_angle_3_deg 12.29 r_sphericity_bonded 10.37 r_dihedral_angle_1_deg 5.476 r_rigid_bond_restr 3.807 r_angle_refined_deg 1.605 r_angle_other_deg 1.097 r_chiral_restr 0.104
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.619 r_sphericity_free 21.536 r_dihedral_angle_4_deg 21.452 r_dihedral_angle_3_deg 12.29 r_sphericity_bonded 10.37 r_dihedral_angle_1_deg 5.476 r_rigid_bond_restr 3.807 r_angle_refined_deg 1.605 r_angle_other_deg 1.097 r_chiral_restr 0.104 r_bond_refined_d 0.013 r_gen_planes_refined 0.009 r_gen_planes_other 0.003 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10999 Nucleic Acid Atoms Solvent Atoms 1226 Heterogen Atoms 262
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing