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DG04279 glycoside hydrolase family 172
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4KQ7 4KQ7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293.15 100 mM MOPS/HEPES pH 7.5, 20 mM 1,6-Hexanediol; 20 mM 1-Butanol
20 mM 1,2-Propanediol; 20 mM 2-Propanol;
20 mM 1,4-Butanediol; 20 mM 1,3-Propanedioalcohol, 20 % Etylene Glycol and 10 % PEG 8000
Crystal Properties Matthews coefficient Solvent content 2.55 51.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.15 α = 90 b = 89.15 β = 90 c = 289.32 γ = 120
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 2020-08-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.9786 Diamond I24
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 1.4 68.112 99.9 0.078 0.086 0.036 0.999 12.7 10.2 87401
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.4 1.42 0.412 6.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 4KQ7 1.4 68.112 87400 4427 99.921 0.163 0.1622 0.1622 0.1839 0.1841 24.541
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] 0.865 0.432 0.865 -2.805
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.712 r_dihedral_angle_3_deg 13.062 r_dihedral_angle_2_deg 12.547 r_dihedral_angle_1_deg 7.685 r_lrange_it 5.223 r_lrange_other 5.174 r_scangle_it 4.584 r_scangle_other 4.584 r_scbond_it 3.162 r_scbond_other 3.161
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.712 r_dihedral_angle_3_deg 13.062 r_dihedral_angle_2_deg 12.547 r_dihedral_angle_1_deg 7.685 r_lrange_it 5.223 r_lrange_other 5.174 r_scangle_it 4.584 r_scangle_other 4.584 r_scbond_it 3.162 r_scbond_other 3.161 r_mcangle_other 2.498 r_mcangle_it 2.497 r_mcbond_it 2.049 r_mcbond_other 2.009 r_angle_refined_deg 1.703 r_angle_other_deg 0.606 r_symmetry_nbd_refined 0.303 r_nbd_refined 0.208 r_nbd_other 0.197 r_symmetry_nbd_other 0.192 r_nbtor_refined 0.184 r_xyhbond_nbd_refined 0.131 r_symmetry_xyhbond_nbd_refined 0.115 r_chiral_restr 0.094 r_symmetry_metal_ion_refined 0.092 r_metal_ion_refined 0.087 r_symmetry_nbtor_other 0.083 r_gen_planes_refined 0.012 r_bond_refined_d 0.011 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3043 Nucleic Acid Atoms Solvent Atoms 208 Heterogen Atoms 4
Software Software Software Name Purpose XDS data scaling xia2 data scaling pointless data scaling Aimless data scaling PHASER phasing Coot model building BUCCANEER model building MolProbity model building REFMAC refinement XDS data reduction