☰ Navigation Tabs
Crystallographic structure of oligosaccharide dehydrogenase from Pycnoporus cinnabarinus, ligand-free form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4YNT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 294 2 M ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 2.35 47.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.874 α = 90 b = 61.592 β = 90 c = 195.091 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 1 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 1.43 97.74 99.9 1 14.5 12.7 103248
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 1.43 1.57 0.79 1.72
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 4YNT 1.6 97.55 103248 74932 3888 99.98 0.16626 0.16467 0.174 0.19648 0.2062 RANDOM 39.759
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] -4.34 4.14 0.2
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.941 r_dihedral_angle_1_deg 15.713 r_dihedral_angle_4_deg 15.521 r_dihedral_angle_3_deg 15.412 r_long_range_B_refined 7.223 r_long_range_B_other 7.133 r_angle_refined_deg 1.713 r_angle_other_deg 1.425 r_scangle_other 1.328 r_mcangle_other 1.134
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.941 r_dihedral_angle_1_deg 15.713 r_dihedral_angle_4_deg 15.521 r_dihedral_angle_3_deg 15.412 r_long_range_B_refined 7.223 r_long_range_B_other 7.133 r_angle_refined_deg 1.713 r_angle_other_deg 1.425 r_scangle_other 1.328 r_mcangle_other 1.134 r_mcangle_it 1.133 r_scbond_it 0.981 r_scbond_other 0.858 r_mcbond_it 0.697 r_mcbond_other 0.696 r_chiral_restr 0.086 r_bond_refined_d 0.013 r_gen_planes_refined 0.01 r_bond_other_d 0.004 r_gen_planes_other 0.001 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 454 Heterogen Atoms 196
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing