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X-ray structure of a L-rhamnose-alpha-1,4-D-glucuronate lyase from Fusarium oxysporum 12S, L-Rha complex at 100K
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7YQS
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 : 36 % (W/V) PEG 1500, 0.1 M TRIS-DCL (PD 8.5), 0.1 M L-RHA
Crystal Properties Matthews coefficient Solvent content 1.98 38.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.313 α = 90 b = 65.23 β = 90 c = 108.224 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 PILATUS 2M-F 2020-02-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NE3A 1.0 Photon Factory AR-NE3A
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 1.06 42.63 100 0.103 0.107 0.029 0.998 11.9 12.5 180680
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 1.06 1.08 100 1.075 1.124 0.323 0.814 2.1 11.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 7YQS 1.06 41.65 1.34 180532 8948 99.97 0.1723 0.1718 0.1715 0.1829 0.1828 15.22
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 13.3804 f_angle_d 0.9037 f_chiral_restr 0.0869 f_plane_restr 0.0062 f_bond_d 0.0047
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3337 Nucleic Acid Atoms Solvent Atoms 458 Heterogen Atoms 108
Software Software Software Name Purpose XDS data reduction Aimless data scaling PHENIX refinement PHENIX phasing