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Crystallographic structure of oligosaccharide dehydrogenase from Pycnoporus cinnabarinus, glucose-bound form
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 294 2 M ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 2.37 48.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.137 α = 90 b = 61.618 β = 90 c = 195.954 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 6M 2019-11-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ELETTRA BEAMLINE 11.2C 1.0 ELETTRA 11.2C
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 1.57 49.04 99.6 0.99 12 6.6 103996
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 1.57 1.67 0.56
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 FOURIER SYNTHESIS THROUGHOUT 1.57 49.04 79572 4200 99.49 0.16358 0.16221 0.1737 0.18889 0.2016 RANDOM 34.753
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] -3.38 3.25 0.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.393 r_dihedral_angle_1_deg 20.238 r_dihedral_angle_4_deg 17.636 r_dihedral_angle_3_deg 15.795 r_long_range_B_refined 5.791 r_long_range_B_other 5.724 r_angle_refined_deg 1.856 r_scangle_other 1.66 r_angle_other_deg 1.438 r_scbond_it 1.311
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.393 r_dihedral_angle_1_deg 20.238 r_dihedral_angle_4_deg 17.636 r_dihedral_angle_3_deg 15.795 r_long_range_B_refined 5.791 r_long_range_B_other 5.724 r_angle_refined_deg 1.856 r_scangle_other 1.66 r_angle_other_deg 1.438 r_scbond_it 1.311 r_mcangle_other 1.259 r_mcangle_it 1.257 r_scbond_other 1.102 r_mcbond_it 0.8 r_mcbond_other 0.783 r_chiral_restr 0.093 r_bond_refined_d 0.013 r_gen_planes_refined 0.01 r_bond_other_d 0.003 r_gen_planes_other 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4399 Nucleic Acid Atoms Solvent Atoms 354 Heterogen Atoms 251
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling REFMAC phasing