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Crystal structure of Glycerol kinase from Elizabethkingia anophelis NUHP1 in complex with ADP and glycerol
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3EZW two domains from PDB entry 3ezw chain D as per MoRDa
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 290 Optimization screen around condition MCSG1-H10, well A4: 100mM HEPES / NaOH pH 7.48, 23.6% PEG 3350: ElanA.00232.a.B1.PW38276 at 20.5mg/ml, 3mM MgCl2 / ADP: additional overnight soak with fresh 4mM MgCl2 / ADP: cryo: 20% EG in soak solution: tray 309736a4: puck pzi3-5.
Crystal Properties Matthews coefficient Solvent content 2.38 48.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.73 α = 90 b = 185.93 β = 105.776 c = 103.46 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 2019-08-01 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 1.95 50 99.7 0.059 0.069 0.998 14.13 3.733 151883 37.921
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 1.95 2 99.8 0.597 0.713 0.667 1.97 3.374
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 two domains from PDB entry 3ezw chain D as per MoRDa 1.95 35.73 1.35 151808 2015 99.81 0.1654 0.1648 0.1663 0.2053 0.2067 0 38.48
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 12.3441 f_angle_d 0.8026 f_chiral_restr 0.0521 f_bond_d 0.0065 f_plane_restr 0.0044
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 15138 Nucleic Acid Atoms Solvent Atoms 1151 Heterogen Atoms 136
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PDB_EXTRACT data extraction MoRDa phasing Coot model building PHENIX model building