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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, 30 seconds soaking time, pH 6.4, VAPOR DIFFUSION, HANGING
DROP, temperature 100K
Crystal Properties Matthews coefficient Solvent content 2.45 49.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.889 α = 90 b = 86.914 β = 107 c = 81.504 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 1.41 50 99.9 0.081 8.1 4.8 146507 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 1.41 1.46 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 1.45 27.12 134875 134875 1373 100 0.1384 0.13801 0.1396 0.1774 0.1778 RANDOM 19.46
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] 0.34 0.11 -0.19 -0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.812 r_dihedral_angle_4_deg 12.837 r_dihedral_angle_3_deg 11.041 r_sphericity_free 6.697 r_dihedral_angle_1_deg 6.144 r_sphericity_bonded 6.028 r_scangle_it 4.459 r_scbond_it 3.311 r_mcangle_it 2.6 r_mcbond_it 1.866
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.812 r_dihedral_angle_4_deg 12.837 r_dihedral_angle_3_deg 11.041 r_sphericity_free 6.697 r_dihedral_angle_1_deg 6.144 r_sphericity_bonded 6.028 r_scangle_it 4.459 r_scbond_it 3.311 r_mcangle_it 2.6 r_mcbond_it 1.866 r_angle_refined_deg 1.848 r_rigid_bond_restr 1.759 r_metal_ion_refined 0.263 r_nbd_refined 0.213 r_xyhbond_nbd_refined 0.182 r_symmetry_hbond_refined 0.166 r_symmetry_vdw_refined 0.147 r_chiral_restr 0.134 r_bond_refined_d 0.024 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 5599 Nucleic Acid Atoms Solvent Atoms 1049 Heterogen Atoms 66
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling