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Crystal structure of a L-rhamnose-alpha-1,4-D-glucuronate lyase from Fusarium oxysporum 12S, Ligand free form
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 293.15 30 % (v/v) PEG 1500, 0.1 M BICINE-NaOH (pH 8.5), 10 % (v/v) 2-propanol, Crystal was soaked into 20 % (v/v) glycerol at 298 K for 1 min
Crystal Properties Matthews coefficient Solvent content 2.03 39.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.113 α = 90 b = 65.267 β = 90 c = 107.008 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 2019-03-02 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 1.05 50 94.2 0.999 39.4 6.2 190044
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 1.05 1.07 0.931
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION SAD THROUGHOUT 1.05 31.3 179860 9565 99.9 0.1515 0.1505 0.1539 0.1706 0.1743 RANDOM 16.018
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 r_dihedral_angle_2_deg 36.024 r_dihedral_angle_4_deg 15.659 r_dihedral_angle_3_deg 10.23 r_dihedral_angle_1_deg 7.384 r_angle_refined_deg 2.23 r_angle_other_deg 1.1 r_chiral_restr 0.138 r_bond_refined_d 0.027 r_gen_planes_refined 0.013 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.024 r_dihedral_angle_4_deg 15.659 r_dihedral_angle_3_deg 10.23 r_dihedral_angle_1_deg 7.384 r_angle_refined_deg 2.23 r_angle_other_deg 1.1 r_chiral_restr 0.138 r_bond_refined_d 0.027 r_gen_planes_refined 0.013 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3337 Nucleic Acid Atoms Solvent Atoms 597 Heterogen Atoms 52
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction HKL-2000 data scaling PHENIX phasing Coot model building