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Crystal structure of Ribokinase from Cryptococcus neoformans var. grubii serotype A in complex with ADP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6CW5 apo structure, 6cw5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 285 Microlytic MCSG-1 screen D12: 20% (w/V) PDG 3350, 200mM ammonium chloride; CrneC.01141.a.B12.PW38396 at 19.46mg/ml + 2.5mM ADP + 2.5mM MgCl2; tray 299998 D12; cryo: 20% EG + 2.5mM ADP/MgCl2; puck pjn0-4
Crystal Properties Matthews coefficient Solvent content 2.28 45.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.17 α = 90 b = 84.57 β = 95.27 c = 98.27 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 CCD RAYONIX MX-300 C(111) 2018-04-12 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 2.5 37.05 99.1 0.046 0.055 0.999 17.97 3.413 43388 58.322
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 2.5 2.56 99.9 0.575 0.682 0.8 2.09 3.427
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT apo structure, 6cw5 2.5 37.05 1.35 43337 1941 99.1 0.1833 0.1811 0.1849 0.2304 0.233 0 65.7744
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 14.991 f_angle_d 0.827 f_chiral_restr 0.048 f_bond_d 0.006 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9027 Nucleic Acid Atoms Solvent Atoms 167 Heterogen Atoms 123
Software Software Software Name Purpose XDS data reduction XSCALE data scaling PHENIX refinement PDB_EXTRACT data extraction PHASER phasing