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Structure of Rhamnosidase from Novosphingobium sp. PP1Y
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 298 0.1 M MES, pH 6.8, 6-7% Tascimate pH 5.0, 2-10 mM Tris, pH 7.5, 10 % w/w PEG 20K, 6-10% glycerol, and 0.01% NaN3
Crystal Properties Matthews coefficient Solvent content 3.16 61.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.809 α = 90 b = 114.57 β = 90 c = 158.797 γ = 90
Symmetry Space Group P 2 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 2018-07-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-2 0.979 SSRL BL12-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) 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 2.20000074944 39.7 99.9 0.092 14.2 6.7 144262 30.4712029358
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.20000074944 2.25 0.462 3.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 SAD FREE R-VALUE 2.20000074944 39.69925 1.89205264243 144262 6975 99.7986897539 0.163541015328 0.162851787376 0.1657 0.177046121509 0.1842 43.4570003117
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 16.3245778265 f_angle_d 1.02650879138 f_chiral_restr 0.0687153025182 f_bond_d 0.00994388297688 f_plane_restr 0.00599732907706
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8079 Nucleic Acid Atoms Solvent Atoms 732 Heterogen Atoms 1
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHENIX phasing