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Crystal structure of glucokinase from Balamuthia mandrillaris in complex with glucose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6DA0 3 domains of PDB entry 6DA0 as per MORDA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 290 8.35 mg/mL BamaA.19900.a.MP3.PS38592 in 2 mM glucose, 2 mM AMPPNP, 2 mM magnesium chloride against RigakuReagents Wizard 3/4 screen, condition E11 (30% v/v PEG300, 200 mM calcium acetate, 100 mM sodium cacodylate/HCl, pH 6.5), direct cryoprotection, tray 311701e11, puck zcg0-8
Crystal Properties Matthews coefficient Solvent content 3.75 67.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 157.3 α = 90 b = 157.3 β = 90 c = 157.3 γ = 90
Symmetry Space Group P 41 3 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 RAYONIX MX-300 2020-02-20 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 2.65 50 99.6 0.091 0.095 0.998 22.86 13.219 19871 50.15
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 2.65 2.72 100 0.605 0.628 0.943 5.16 13.5
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 FREE R-VALUE 3 domains of PDB entry 6DA0 as per MORDA 2.65 49.74 1.36 19851 2052 99.73 0.1774 0.1743 0.1755 0.2039 0.2023 0 49.41
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 20.1587 f_angle_d 0.7551 f_chiral_restr 0.0446 f_bond_d 0.0054 f_plane_restr 0.0048
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2824 Nucleic Acid Atoms Solvent Atoms 67 Heterogen Atoms 19
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PDB_EXTRACT data extraction MoRDa phasing Coot model building