☰ Navigation Tabs
Crystal structure of GH65 alpha-1,2-glucosidase from Flavobacterium johnsoniae in complex with glucose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7FE3
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% PEG3350
Crystal Properties Matthews coefficient Solvent content 2.62 53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 123.505 α = 90 b = 194.201 β = 116.598 c = 112.006 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 2020-11-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 0.9795 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 1.4 50 98 0.06 0.065 0.025 0.999 15.6 6.8 451842
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 1.4 1.48 96.6 0.755 0.82 0.318 0.81 2.4 6.5
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 7FE3 1.4 44.704 451583 22421 97.986 0.157 0.1566 0.1602 0.1702 0.1736 25.135
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] -0.073 0.105 0.162 -0.129
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.912 r_dihedral_angle_4_deg 13.57 r_dihedral_angle_3_deg 13.065 r_dihedral_angle_1_deg 6.866 r_lrange_it 4.721 r_lrange_other 4.6 r_scangle_it 1.745 r_scangle_other 1.745 r_angle_refined_deg 1.526 r_angle_other_deg 1.454
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.912 r_dihedral_angle_4_deg 13.57 r_dihedral_angle_3_deg 13.065 r_dihedral_angle_1_deg 6.866 r_lrange_it 4.721 r_lrange_other 4.6 r_scangle_it 1.745 r_scangle_other 1.745 r_angle_refined_deg 1.526 r_angle_other_deg 1.454 r_scbond_it 1.131 r_scbond_other 1.131 r_mcangle_it 0.979 r_mcangle_other 0.979 r_mcbond_it 0.612 r_mcbond_other 0.612 r_symmetry_nbd_refined 0.321 r_nbd_refined 0.209 r_nbd_other 0.202 r_symmetry_nbd_other 0.175 r_nbtor_refined 0.172 r_symmetry_xyhbond_nbd_refined 0.128 r_xyhbond_nbd_refined 0.112 r_symmetry_nbtor_other 0.079 r_chiral_restr 0.078 r_bond_refined_d 0.009 r_gen_planes_refined 0.009 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 15741 Nucleic Acid Atoms Solvent Atoms 1668 Heterogen Atoms 144
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling MOLREP phasing Coot model building