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E. coli adenylate kinase in complex with two ADP molecules as a result of enzymatic AP4A hydrolysis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other unpublished structure from earlier data collection
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 291.15 20 % (w/v) PEG 3350, 100 mM Bis-tris propane pH 6.5
Crystal Properties Matthews coefficient Solvent content 2.77 55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.81 α = 90 b = 77.36 β = 95.484 c = 59.6 γ = 90
Symmetry Space Group P 1 21 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 2020-07-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX IV BEAMLINE BioMAX 0.976254 MAX IV BioMAX
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim 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 1.49 37.61 99.2 0.034 0.043 0.023 0.999 15.31 3.4 285900 30.67
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.49 1.53 98.9 0.868 1.085 0.542 0.515 1.53 3.4
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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.49 37.61 83049 2076 99.19 0.1639 0.1632 0.1695 0.1907 0.1891 32.74
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 19.8478 f_angle_d 1.2967 f_chiral_restr 0.0771 f_plane_restr 0.0197 f_bond_d 0.0093
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3312 Nucleic Acid Atoms Solvent Atoms 492 Heterogen Atoms 121
Software Software Software Name Purpose MxCuBE data collection XDS data reduction XSCALE data scaling MOLREP phasing Coot model building REFMAC refinement PHENIX refinement