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Crystal structure of apo-GltTk obtained with in meso crystallization (P6322 space group)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5DWY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 LIPIDIC CUBIC PHASE 4.9 293 1 M ammonium sulfate
100 mM sodium acetate
Crystal Properties Matthews coefficient Solvent content 3.44 64.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 94.24 α = 90 b = 94.24 β = 90 c = 244.56 γ = 120
Symmetry Space Group P 63 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 PIXEL DECTRIS EIGER X 16M 2022-05-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.97242 PETRA III, EMBL c/o DESY P13 (MX1)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 3.2 50 92.6 0.322 0.998 12.95 36.9 10342 101.55
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.2 3.3 0.999 3.968 0.585 1.14 39.1
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 3.2 47.12 1.34 10341 516 91.35 0.2934 0.2923 0.2927 0.3124 0.3127 102.52
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 13.7116 f_angle_d 0.7292 f_chiral_restr 0.0435 f_plane_restr 0.008 f_bond_d 0.0038
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2994 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 75
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling PHASER phasing