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Crystal structure of chondroitin ABC lyase I in complex with chondroitin disaccharide 0S
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1HN0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 magnesium acetate, ammonium acetate, polyethylene glycol 3350, HEPES-Na
Crystal Properties Matthews coefficient Solvent content 2.29 46.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.786 α = 90 b = 94.29 β = 90 c = 228.989 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 S 6M 2020-12-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.0 Photon Factory BL-5A
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 2.5 50 99.9 0.176 0.993 8.2 6.5 37662
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 2.5 2.6 99.9 0.972 0.835 2.2 6.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 1HN0 2.5 48.98 35756 1830 99.91 0.2071 0.2036 0.2107 0.2778 0.2789 RANDOM 45.303
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] 1.29 1.77 -3.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.633 r_dihedral_angle_3_deg 18.22 r_dihedral_angle_4_deg 17.441 r_dihedral_angle_1_deg 8.678 r_angle_refined_deg 1.85 r_angle_other_deg 1.281 r_chiral_restr 0.077 r_bond_refined_d 0.011 r_gen_planes_refined 0.008 r_gen_planes_other 0.003
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.633 r_dihedral_angle_3_deg 18.22 r_dihedral_angle_4_deg 17.441 r_dihedral_angle_1_deg 8.678 r_angle_refined_deg 1.85 r_angle_other_deg 1.281 r_chiral_restr 0.077 r_bond_refined_d 0.011 r_gen_planes_refined 0.008 r_gen_planes_other 0.003 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7720 Nucleic Acid Atoms Solvent Atoms 99 Heterogen Atoms 53
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction Aimless data scaling MOLREP phasing