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Crystal structure of Arthrobacter aurescens chondroitin AC lyase
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 6.4 293 PEG 8000, ammonium acetate, glycerol, phosphate buffer, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.43 49.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.679 α = 90 b = 86.437 β = 106.88 c = 81.289 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 2002-10-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X8C 0.9798 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 1.9 50 100 0.75 7.3 3.9 60174 60174 1 1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 1.97 100 0.65 2.8
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 1.9 29.36 59116 59116 1031 100 0.19135 0.19035 0.1909 0.25178 0.2493 RANDOM 23.308
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] -0.32 0.96 -1 1.88
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.289 r_dihedral_angle_4_deg 14.364 r_dihedral_angle_3_deg 13.09 r_dihedral_angle_1_deg 6.706 r_scangle_it 3.444 r_scbond_it 2.386 r_angle_refined_deg 1.677 r_mcangle_it 1.501 r_mcbond_it 0.923 r_nbd_refined 0.215
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.289 r_dihedral_angle_4_deg 14.364 r_dihedral_angle_3_deg 13.09 r_dihedral_angle_1_deg 6.706 r_scangle_it 3.444 r_scbond_it 2.386 r_angle_refined_deg 1.677 r_mcangle_it 1.501 r_mcbond_it 0.923 r_nbd_refined 0.215 r_xyhbond_nbd_refined 0.187 r_symmetry_hbond_refined 0.161 r_symmetry_vdw_refined 0.144 r_chiral_restr 0.114 r_metal_ion_refined 0.1 r_bond_refined_d 0.018 r_gen_planes_refined 0.008 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 r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5600 Nucleic Acid Atoms Solvent Atoms 837 Heterogen Atoms 38
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling