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Neutron structure of a L-rhamnose-alpha-1,4-D-glucuronate lyase from Fusarium oxysporum 12S, L-Rha complex
X-RAY DIFFRACTION - NEUTRON DIFFRACTION
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7ESK 7esk 7esk
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 Protein solution : protein 24mg/ml, 20mM Tris-DCl (pD 8.0), Reservoir solution : 33 % (w/v) PEG 1500, 0.1 M Tris-DCl (pD 8.5), 0.1 M L-Rha
Crystal Properties Matthews coefficient Solvent content 2.07 40.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.78 α = 90 b = 65.8 β = 90 c = 108.95 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 293 PIXEL DECTRIS PILATUS3 S 6M 2021-03-17 M SINGLE WAVELENGTH 2 1 neutron 293 DIFFRACTOMETER iBIX 2021-02-12 L LAUE
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.0 Photon Factory BL-5A 2 SPALLATION SOURCE J-PARC MLF BEAMLINE BL-03 2.28-6.19 JPARC MLF BL-03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) R Split (All) 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 1.25 43.42 100 0.059 0.025 0.999 15 6.4 115388 14.58 2 1.8 19.82 98.9 0.257 0.096 0.983 8.4 7.9 38826 -3 14.58
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) R Split (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.25 1.27 0.886 0.38 0.794 2.2 6.4 2 1.8 1.86 1.174 0.507 0.411 1.6 5.9
Refinement Statistics Diffraction ID Structure Solution Method Resolution (High) Resolution (Low) Cut-off Sigma (I) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 1.25 43.42 1.33 115291 5764 99.96 0.1474 0.1465 0.1483 0.163 0.1635 33.31 NEUTRON DIFFRACTION MOLECULAR REPLACEMENT 1.8 19.82 38824 1946 99 0.1634 0.1619 0.1907
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 15.2464 f_angle_d 1.1603 f_chiral_restr 0.0911 f_bond_d 0.0071 f_plane_restr 0.0058
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3337 Nucleic Acid Atoms Solvent Atoms 299 Heterogen Atoms 108
Software Software Software Name Purpose XDS data reduction Aimless data scaling PHENIX phasing PHENIX refinement