☰ Navigation Tabs
Crystal structure of GH65 alpha-1,2-glucosidase from Flavobacterium johnsoniae
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 300 mM ammonium citrate, pH 7.0-8.0, 10 mM TCEP, 12% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.59 52.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 122.83 α = 90 b = 193.97 β = 116.601 c = 111.735 γ = 90
Symmetry Space Group C 1 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 100 PIXEL DECTRIS PILATUS3 S 2M 2021-06-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1.0 Photon Factory AR-NW12A
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 1.54 50 99.7 0.05 0.054 0.021 1 19.9 6.8 342453
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 1.54 1.62 0.916 0.992 0.379 0.846 2.3
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 SAD FREE R-VALUE 1.54 48.54 340941 16770 99.292 0.172 0.1709 0.1815 0.1918 0.2011 29.102
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] -0.698 0.791 -1.879 1.188
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.817 r_dihedral_angle_3_deg 13.173 r_dihedral_angle_4_deg 13.15 r_dihedral_angle_1_deg 6.849 r_lrange_it 4.164 r_lrange_other 4.073 r_scangle_it 2.398 r_scangle_other 2.398 r_scbond_it 1.54 r_scbond_other 1.54
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.817 r_dihedral_angle_3_deg 13.173 r_dihedral_angle_4_deg 13.15 r_dihedral_angle_1_deg 6.849 r_lrange_it 4.164 r_lrange_other 4.073 r_scangle_it 2.398 r_scangle_other 2.398 r_scbond_it 1.54 r_scbond_other 1.54 r_angle_refined_deg 1.501 r_mcangle_it 1.477 r_mcangle_other 1.477 r_angle_other_deg 1.416 r_mcbond_it 0.983 r_mcbond_other 0.983 r_symmetry_nbd_refined 0.247 r_nbd_refined 0.208 r_symmetry_nbd_other 0.173 r_nbtor_refined 0.171 r_nbd_other 0.149 r_symmetry_xyhbond_nbd_refined 0.133 r_xyhbond_nbd_refined 0.113 r_chiral_restr 0.08 r_symmetry_nbtor_other 0.077 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_symmetry_xyhbond_nbd_other 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 15741 Nucleic Acid Atoms Solvent Atoms 1452 Heterogen Atoms 104
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling PHASER phasing Coot model building