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Amicoumacin kinase hAmiN in complex with AMP-PNP, MG2+ and Ami
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 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 Mg2+
Crystal Properties Matthews coefficient Solvent content 2.64 53.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.66 α = 112.29 b = 66 β = 102.81 c = 70.41 γ = 94.79
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-F KB Mirrors 2019-06-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.976 PETRA III, EMBL c/o DESY P13 (MX1)
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 12 95.6 0.087 0.094 0.998 11.1 6.85 177497 14.4
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 93.7 1.091 1.05 0.686 7.07
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 12 161039 8575 95.42 0.1461 0.1445 0.145 0.1762 0.1763 RANDOM 19.436
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] 0.5 0.04 0.07 -0.13 -0.13 -0.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.804 r_sphericity_free 23.002 r_dihedral_angle_4_deg 20.916 r_dihedral_angle_3_deg 12.515 r_sphericity_bonded 8.154 r_dihedral_angle_1_deg 5.58 r_rigid_bond_restr 2.562 r_angle_refined_deg 1.535 r_angle_other_deg 1.077 r_chiral_restr 0.096
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.804 r_sphericity_free 23.002 r_dihedral_angle_4_deg 20.916 r_dihedral_angle_3_deg 12.515 r_sphericity_bonded 8.154 r_dihedral_angle_1_deg 5.58 r_rigid_bond_restr 2.562 r_angle_refined_deg 1.535 r_angle_other_deg 1.077 r_chiral_restr 0.096 r_bond_refined_d 0.011 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 5559 Nucleic Acid Atoms Solvent Atoms 788 Heterogen Atoms 137
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XSCALE data scaling MOLREP phasing