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Crystal structure of glucokinase (NfHK) from Naegleria fowleri
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5BRH PDB entries 5BRH & 1SZ2 experimental model PDB 1SZ2 PDB entries 5BRH & 1SZ2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 290 13.78 mg/mL NafoA.19900.a.B11.PW39443 + 2 mM magnesium chloride, AMPPNP, beta-D-glucose + Molecular Dimensions Morpheus screen, C8 (12.5% w/v PEG1000, 12.5% w/v PEG3350, 12.5% v/v MPD, 30 mM sodium nitrate, 0.3 M disodium hydrogen phosphate, 0.3 M ammonium sulfate, 100 mM bicine/Trizma base, pH 8.5), cryoprotection: direct, tray 299931c8, puck VSZ1-5
Crystal Properties Matthews coefficient Solvent content 3.5 65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 202.48 α = 90 b = 202.48 β = 90 c = 68.79 γ = 90
Symmetry Space Group I 4 2 2
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 RIGAKU SATURN 944+ 2018-04-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E+ SUPERBRIGHT 1.5418
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 2.2 45.276 99.6 0.09 0.097 0.999 17.95 7.108 36362 28.81
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 2.26 99.7 0.572 0.633 0.868 3.27 5.296
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 PDB entries 5BRH & 1SZ2 2.2 45.276 1.34 36357 2015 99.64 0.1557 0.1539 0.1555 0.1872 0.1849 0 35.4694
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]
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2994 Nucleic Acid Atoms Solvent Atoms 365 Heterogen Atoms 43
Software Software Software Name Purpose XDS data reduction XSCALE data scaling PHENIX refinement PDB_EXTRACT data extraction PHASER phasing MoRDa phasing PARROT phasing ARP/wARP model building BUCCANEER model building Coot model building