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Crystallographic structure of oligosaccharide dehydrogenase from Pycnoporus cinnabarinus, laminaribiose-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 2.31 46.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.914 α = 90 b = 60.929 β = 90 c = 194.286 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 6M 2019-06-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.9685 Diamond I24
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 1.75 97.33 99.9 0.99 7 13 59350
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 1.75 2.02 0.81
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT 1.75 97.33 56520 3022 99.84 0.16977 0.16777 0.20729 0.1997 RANDOM 45.779
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] -2.74 3.9 -1.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.978 r_dihedral_angle_4_deg 19.05 r_dihedral_angle_3_deg 16.938 r_dihedral_angle_1_deg 16.816 r_long_range_B_refined 5.393 r_long_range_B_other 5.217 r_scangle_other 2.829 r_mcangle_other 2.2 r_mcangle_it 2.199 r_angle_refined_deg 2.005
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.978 r_dihedral_angle_4_deg 19.05 r_dihedral_angle_3_deg 16.938 r_dihedral_angle_1_deg 16.816 r_long_range_B_refined 5.393 r_long_range_B_other 5.217 r_scangle_other 2.829 r_mcangle_other 2.2 r_mcangle_it 2.199 r_angle_refined_deg 2.005 r_scbond_it 1.976 r_scbond_other 1.895 r_mcbond_it 1.569 r_mcbond_other 1.568 r_angle_other_deg 1.436 r_chiral_restr 0.098 r_bond_refined_d 0.014 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 302 Heterogen Atoms 242
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling REFMAC phasing