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E. Coli Glucokinase - K216Q
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1Q18
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 297 100 mM MES / Sodium hydroxide pH 5.5, 100 mM Ammonium citrate dibasic, 20% (w/v) PEG 3350, and 5% (v/v) 2-Propanol
Crystal Properties Matthews coefficient Solvent content 2.77 55.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.088 α = 90 b = 85.088 β = 90 c = 183.319 γ = 120
Symmetry Space Group P 32 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 297 PIXEL RIGAKU HyPix-6000HE 2025-06-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SEALED TUBE RIGAKU PhotonJet-S 1.54
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim 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 2.44 28.72 99.9 0.372 0.393 0.126 0.99 5.6 9.5 29374
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.44 2.54 100 5.557 5.856 1.824 0.211 10.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 FREE R-VALUE 2.44 28.72 0.01 25690 1246 87.53 0.1808 0.1785 0.1789 0.2248 0.2253
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 11.311 f_angle_d 0.424 f_chiral_restr 0.041 f_plane_restr 0.004 f_bond_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4874 Nucleic Acid Atoms Solvent Atoms 89 Heterogen Atoms 10
Software Software Software Name Purpose PHENIX refinement PDB_EXTRACT data extraction CrysalisPro data reduction Aimless data scaling PHENIX phasing