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Central domain of Glucan Water Dikinase-1 in alternative closed conformation
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9HA9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 285 0.1 M HEPES Na salt pH 7.5, 0.7 M tri-Na citrate
Crystal Properties Matthews coefficient Solvent content 3.18 61.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 94.134 α = 90 b = 94.134 β = 90 c = 150.757 γ = 90
Symmetry Space Group P 43 21 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 PILATUS 6M 2022-05-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.8856 ESRF ID23-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 3.25 49.89 100 0.046 0.999 5 12.7 11258
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.25 3.43 0.749 0.966 1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3.25 47.111 11212 531 99.875 0.263 0.2607 0.2645 0.3061 0.3103 193.159
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] 1.877 1.877 -3.754
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.393 r_dihedral_angle_6_deg 12.146 r_lrange_it 11.029 r_lrange_other 11.029 r_dihedral_angle_1_deg 5.941 r_scangle_it 5.491 r_scangle_other 5.49 r_mcangle_it 5.263 r_mcangle_other 5.262 r_dihedral_angle_2_deg 3.844
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.393 r_dihedral_angle_6_deg 12.146 r_lrange_it 11.029 r_lrange_other 11.029 r_dihedral_angle_1_deg 5.941 r_scangle_it 5.491 r_scangle_other 5.49 r_mcangle_it 5.263 r_mcangle_other 5.262 r_dihedral_angle_2_deg 3.844 r_scbond_it 3.187 r_scbond_other 3.186 r_mcbond_it 3.171 r_mcbond_other 3.171 r_angle_refined_deg 0.959 r_angle_other_deg 0.355 r_symmetry_nbd_refined 0.253 r_nbd_refined 0.241 r_nbd_other 0.233 r_symmetry_nbd_other 0.188 r_nbtor_refined 0.18 r_xyhbond_nbd_refined 0.168 r_symmetry_xyhbond_nbd_refined 0.153 r_symmetry_nbtor_other 0.072 r_symmetry_xyhbond_nbd_other 0.071 r_chiral_restr 0.045 r_gen_planes_refined 0.003 r_bond_refined_d 0.002 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3462 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing