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Crystal structure of Arthrobacter aurescens chondroitin AC lyase in complex with chondroitin tetrasaccharide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1RW9 PDB entry 1RW9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.4 PEG 8000, ammonium acetate, glycerol, phosphate buffer, 10 minutes soaking time, pH 6.4, VAPOR DIFFUSION, HANGING
DROP, temperature 100K
Crystal Properties Matthews coefficient Solvent content 2.41 48.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.683 α = 90 b = 86.449 β = 106.87 c = 80.566 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 4 2002-06-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X8C 0.9787 NSLS X8C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) 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 1.5 50 99.9 0.077 9.2 3.8 120769 1 1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.5 1.55 99.9
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 PDB entry 1RW9 1.5 28.06 119480 119480 1221 100 0.13664 0.13629 0.1372 0.17267 0.1715 RANDOM 18.336
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] 0.55 0.33 -0.31 -0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.33 r_dihedral_angle_4_deg 13.834 r_dihedral_angle_3_deg 11.059 r_sphericity_free 6.262 r_dihedral_angle_1_deg 6.1 r_sphericity_bonded 5.558 r_scangle_it 4.291 r_scbond_it 3.186 r_mcangle_it 2.47 r_angle_refined_deg 1.832
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.33 r_dihedral_angle_4_deg 13.834 r_dihedral_angle_3_deg 11.059 r_sphericity_free 6.262 r_dihedral_angle_1_deg 6.1 r_sphericity_bonded 5.558 r_scangle_it 4.291 r_scbond_it 3.186 r_mcangle_it 2.47 r_angle_refined_deg 1.832 r_mcbond_it 1.775 r_rigid_bond_restr 1.7 r_metal_ion_refined 0.216 r_nbd_refined 0.211 r_symmetry_hbond_refined 0.201 r_xyhbond_nbd_refined 0.183 r_chiral_restr 0.126 r_symmetry_vdw_refined 0.125 r_bond_refined_d 0.021 r_gen_planes_refined 0.011 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_mcbond_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5600 Nucleic Acid Atoms Solvent Atoms 1061 Heterogen Atoms 66
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling