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Central domain fragment of Glucan Water Dikinase-1 from S.tuberosum
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 285 2 M NaCl, 10 % PEG 6K
Crystal Properties Matthews coefficient Solvent content 3.02 59.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 110.312 α = 90 b = 110.312 β = 90 c = 209.177 γ = 90
Symmetry Space Group P 41 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 2022-09-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.9793 ALBA XALOC
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 50 100 0.102 3.1 25.9 26669
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3 3.16 0.742
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 50 26625 1336 99.985 0.216 0.2146 0.2115 0.2381 0.2334 113.608
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] 2.112 2.112 -4.224
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.032 r_dihedral_angle_6_deg 11.708 r_lrange_it 5.933 r_lrange_other 5.932 r_dihedral_angle_1_deg 5.614 r_dihedral_angle_2_deg 4.808 r_mcangle_it 2.534 r_mcangle_other 2.534 r_scangle_it 2.465 r_scangle_other 2.465
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.032 r_dihedral_angle_6_deg 11.708 r_lrange_it 5.933 r_lrange_other 5.932 r_dihedral_angle_1_deg 5.614 r_dihedral_angle_2_deg 4.808 r_mcangle_it 2.534 r_mcangle_other 2.534 r_scangle_it 2.465 r_scangle_other 2.465 r_mcbond_it 1.481 r_mcbond_other 1.48 r_scbond_it 1.4 r_scbond_other 1.399 r_angle_refined_deg 0.899 r_angle_other_deg 0.34 r_nbd_refined 0.211 r_symmetry_nbd_other 0.175 r_nbtor_refined 0.174 r_symmetry_xyhbond_nbd_refined 0.166 r_xyhbond_nbd_refined 0.148 r_nbd_other 0.139 r_symmetry_nbd_refined 0.137 r_symmetry_nbtor_other 0.07 r_ncsr_local_group_1 0.061 r_chiral_restr 0.044 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 7081 Nucleic Acid Atoms Solvent Atoms 53 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing