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Crystallographic structure of oligosaccharide dehydrogenase from Pycnoporus cinnabarinus bound to Sinapic Acid, orthorhombic 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 2.37 48.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.06 α = 90 b = 61.883 β = 90 c = 195.597 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 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) R Merge I (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 1.19 97.99 95.6 0.076 0.999 14 12.8 129361
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.19 1.297 1.119 0.702 1.7
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 MOLECULAR REPLACEMENT THROUGHOUT 1.3 97.99 116481 6054 83.21 0.1443 0.14251 0.1452 0.17824 0.1804 RANDOM 28.177
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] 1.3 -2.46 1.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.592 r_dihedral_angle_4_deg 18.506 r_dihedral_angle_3_deg 14.802 r_dihedral_angle_1_deg 7.247 r_rigid_bond_restr 7.104 r_long_range_B_refined 3.353 r_long_range_B_other 3.128 r_scangle_other 2.15 r_angle_refined_deg 1.746 r_scbond_it 1.716
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.592 r_dihedral_angle_4_deg 18.506 r_dihedral_angle_3_deg 14.802 r_dihedral_angle_1_deg 7.247 r_rigid_bond_restr 7.104 r_long_range_B_refined 3.353 r_long_range_B_other 3.128 r_scangle_other 2.15 r_angle_refined_deg 1.746 r_scbond_it 1.716 r_scbond_other 1.715 r_mcangle_other 1.587 r_mcangle_it 1.586 r_angle_other_deg 1.486 r_mcbond_it 1.18 r_mcbond_other 1.167 r_chiral_restr 0.096 r_bond_refined_d 0.012 r_gen_planes_refined 0.011 r_bond_other_d 0.006 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_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4410 Nucleic Acid Atoms Solvent Atoms 665 Heterogen Atoms 193
Software Software Software Name Purpose REFMAC refinement XDS data reduction STARANISO data scaling MOLREP phasing