☰ Navigation Tabs
Crystal structure of a novel 4-O-alpha-L-rhamnosyl-beta-D-glucuronidase from Fusarium oxysporum 12S - Rha-GlcA complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7DFQ FoBGlcA ligand-free
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 293.15 30% (v/v) PEG mme 2000, 0.1 M MES-NaOH (pH 6.0), crystal was soaked into 20 mM Rha-GlcA and 20% glycerol at 298K for 5 min
Crystal Properties Matthews coefficient Solvent content 2.23 44.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.682 α = 90 b = 78.567 β = 90 c = 127.425 γ = 90
Symmetry Space Group P 21 21 21
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 6M 2019-06-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.000 Photon Factory BL-5A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.49 49.54 99.6 0.996 23.1 4.54 70690
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 1.49 1.52 0.681 1.5
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT FoBGlcA ligand-free 1.49 49.49 67062 3549 99.57 0.1478 0.1463 0.1493 0.1763 0.1797 RANDOM 22.45
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] -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.446 r_dihedral_angle_4_deg 17.077 r_dihedral_angle_3_deg 12.109 r_dihedral_angle_1_deg 6.479 r_angle_other_deg 3.911 r_angle_refined_deg 1.864 r_chiral_restr 0.099 r_gen_planes_other 0.022 r_bond_refined_d 0.016 r_gen_planes_refined 0.011
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.446 r_dihedral_angle_4_deg 17.077 r_dihedral_angle_3_deg 12.109 r_dihedral_angle_1_deg 6.479 r_angle_other_deg 3.911 r_angle_refined_deg 1.864 r_chiral_restr 0.099 r_gen_planes_other 0.022 r_bond_refined_d 0.016 r_gen_planes_refined 0.011 r_bond_other_d
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3380 Nucleic Acid Atoms Solvent Atoms 546 Heterogen Atoms 85
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction Aimless data scaling MOLREP phasing Coot model building