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Crystal structure of ligand-free chondroitin ABC lyase I
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 46.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.944 α = 90 b = 94.239 β = 90 c = 229.082 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 2M 2020-11-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1.0 Photon Factory AR-NW12A
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 1.88 50 100 0.135 0.994 8.8 6.5 87389
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 1.88 1.91 100 0.871 0.73 2 6.5
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 1.88 43.47 82946 4349 99.95 0.1711 0.169 0.1793 0.2128 0.218 RANDOM 27.116
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] 0.38 1.24 -1.62
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.873 r_dihedral_angle_4_deg 19.452 r_dihedral_angle_3_deg 15.064 r_dihedral_angle_1_deg 7.617 r_angle_refined_deg 1.798 r_angle_other_deg 1.45 r_chiral_restr 0.09 r_bond_refined_d 0.014 r_gen_planes_refined 0.011 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.873 r_dihedral_angle_4_deg 19.452 r_dihedral_angle_3_deg 15.064 r_dihedral_angle_1_deg 7.617 r_angle_refined_deg 1.798 r_angle_other_deg 1.45 r_chiral_restr 0.09 r_bond_refined_d 0.014 r_gen_planes_refined 0.011 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7720 Nucleic Acid Atoms Solvent Atoms 787 Heterogen Atoms 9
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction Aimless data scaling MOLREP phasing