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Amicoumacin kinase hAmiN in complex with AMP-PNP, Ca2+ and Ami
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 0.1 M MES pH6.5
0.2 M NaOAc
27-29% (w/v) PEG 2000MME
2 mM amiA
2.2 mM AMP-PNP
20 mM Ca2+
Crystal Properties Matthews coefficient Solvent content 2.59 52.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 126.64 α = 90 b = 54.46 β = 113.28 c = 64.63 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 EIGER X 16M Be CRLs 2019-06-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2) 0.980 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 60 97 0.086 0.089 0.999 13.5 13.8 88781
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 95 2.77 2.87 0.681 2 14.1
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 59.37 81731 4362 96.97 0.1433 0.1415 0.1434 0.1759 0.1774 RANDOM 26.422
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] -1.14 -0.75 1.27 0.37
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.543 r_sphericity_free 23.699 r_dihedral_angle_4_deg 14.316 r_dihedral_angle_3_deg 13.288 r_sphericity_bonded 11.484 r_rigid_bond_restr 5.536 r_dihedral_angle_1_deg 5.089 r_angle_refined_deg 1.524 r_angle_other_deg 1.076 r_chiral_restr 0.093
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.543 r_sphericity_free 23.699 r_dihedral_angle_4_deg 14.316 r_dihedral_angle_3_deg 13.288 r_sphericity_bonded 11.484 r_rigid_bond_restr 5.536 r_dihedral_angle_1_deg 5.089 r_angle_refined_deg 1.524 r_angle_other_deg 1.076 r_chiral_restr 0.093 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 r_gen_planes_other 0.003 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2764 Nucleic Acid Atoms Solvent Atoms 353 Heterogen Atoms 63
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XSCALE data scaling MOLREP phasing