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ADP-dependent kinase complex with fructose-6-phosphate and ADPbetaS
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6C8Z
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.2 292 Protein Condition: F6P 6 mM, mM ADPbs 2.4 mM, MgCl2 7.4 mM , HEPES 25 mM pH 7.8, NaCl 200 mM and 2-mercaptoethanol 1 mM; Reservoir Condition: PEG 20,000 8.4% w/V, MgCl2 0.2M, Sodium citrate 0.1M pH 4.5
Crystal Properties Matthews coefficient Solvent content 2.53 51.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.574 α = 90 b = 79.589 β = 90 c = 108.574 γ = 90
Symmetry Space Group P 21 21 21
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 2M 2017-12-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON LNLS BEAMLINE W01B-MX2 1.45867 LNLS W01B-MX2
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 3.12 44.85 98.3 0.1507 0.1574 0.04486 0.996 16.5 12.4 10902 88.84
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 3.12 3.23 99.53 0.841 0.879 0.2532 0.9 3.02 12.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 6C8Z 3.12 44.85 1.35 10725 536 98.35 0.2426 0.241 0.2441 0.2717 0.2751 85.77
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 18.3728 f_angle_d 0.7422 f_chiral_restr 0.0513 f_plane_restr 0.0071 f_bond_d 0.0045
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3540 Nucleic Acid Atoms Solvent Atoms 5 Heterogen Atoms 44
Software Software Software Name Purpose PHENIX refinement MxCuBE data collection XDS data reduction Aimless data scaling MOLREP phasing