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Crystallographic structure of oligosaccharide dehydrogenase from Pycnoporus cinnabarinus bound to Sinapic Acid, tetragonal crystal
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6XUU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 294 2 M AMMONIUM SULFATE
Crystal Properties Matthews coefficient Solvent content 2.88 57.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 147.531 α = 90 b = 147.531 β = 90 c = 142.79 γ = 90
Symmetry Space Group P 42 21 2
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 EIGER X 9M 2021-09-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 2 0.98011 SOLEIL PROXIMA 2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.86 49.05 100 0.097 0.996 8.4 27.6 131815
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.86 1.89 100 1.789 0.336 0.8 28.5
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-Work (Depositor) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.86 49.04 131734 6685 100 0.169 0.202 0.1791 26.62
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] -0.006 -0.006 0.013
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 19.219 r_dihedral_angle_3_deg 16.218 r_dihedral_angle_1_deg 6.753 r_scangle_it 4.514 r_scbond_it 2.92 r_mcangle_it 2.392 r_angle_refined_deg 2.049 r_mcbond_it 1.689 r_nbtor_refined 0.304 r_xyhbond_nbd_refined 0.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 19.219 r_dihedral_angle_3_deg 16.218 r_dihedral_angle_1_deg 6.753 r_scangle_it 4.514 r_scbond_it 2.92 r_mcangle_it 2.392 r_angle_refined_deg 2.049 r_mcbond_it 1.689 r_nbtor_refined 0.304 r_xyhbond_nbd_refined 0.21 r_nbd_refined 0.206 r_chiral_restr 0.112 r_bond_refined_d 0.015 r_gen_planes_refined 0.015 r_bond_other_d r_angle_other_deg r_dihedral_angle_4_deg r_gen_planes_other r_nbd_other r_nbtor_other 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_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8820 Nucleic Acid Atoms Solvent Atoms 1146 Heterogen Atoms 516
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing