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Co-crystal structure of adenylyl-sulfate kinase from Cryptococcus neoformans bound to ADP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6B8V PDB entry 6B8V
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 290 18.6 mg/mL CrneC.00830.a.B1, PS38292 with JCSG+ A8 (0.2 M ammonium formate, 20% w/v PEG3350, 5 mM magnesium chloride, 5 mM ADP), cryoprotectant: 20% ethylene glycol, 5 mM magnesium chloride, 5 mM ADP, tray 295929, puck gmh8-1
Crystal Properties Matthews coefficient Solvent content 2.7 54.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.33 α = 90 b = 86.33 β = 90 c = 160.81 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MARMOSAIC 225 mm CCD Beryllium Lenses 2017-11-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
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 2 30.662 99.9 0.058 0.067 0.998 14.5 3.84 90486 33.99
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 2 2.05 99.9 0.575 0.667 0.707 2.25 3.855
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 THROUGHOUT PDB entry 6B8V 2 30.662 2.01 90466 1946 99.89 0.2252 0.2243 0.2267 0.2672 0.2729 47.9353
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 13.555 f_angle_d 0.976 f_chiral_restr 0.058 f_bond_d 0.008 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8838 Nucleic Acid Atoms Solvent Atoms 403 Heterogen Atoms 174
Software Software Software Name Purpose XSCALE data scaling PHENIX refinement PDB_EXTRACT data extraction XDS data reduction MOLREP phasing