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Crystal structure of the Arthrobacter aurescens chondroitin AC lyase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other Hg-derivative of the same protein
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.4 293 PEG 8000, ammonium acetate, phosphate buffer, glycerol, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.39 48.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.569 α = 90 b = 86.455 β = 106.9 c = 80.483 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 2002-02-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X8C 0.95 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 1.3 50 96.4 0.094 8.6 7.3 178066 178066 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 1.3 1.35 93.4 3.4
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 Hg-derivative of the same protein 1.35 36.04 158129 158129 1603 100 0.1307 0.13028 0.1309 0.17503 0.1737 RANDOM 13.903
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] 1.05 0.66 -0.26 -0.41
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.765 r_dihedral_angle_4_deg 12.525 r_dihedral_angle_3_deg 10.636 r_sphericity_free 8.983 r_sphericity_bonded 7.594 r_dihedral_angle_1_deg 6.202 r_scangle_it 4.482 r_scbond_it 3.386 r_angle_other_deg 2.982 r_mcangle_it 2.792
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.765 r_dihedral_angle_4_deg 12.525 r_dihedral_angle_3_deg 10.636 r_sphericity_free 8.983 r_sphericity_bonded 7.594 r_dihedral_angle_1_deg 6.202 r_scangle_it 4.482 r_scbond_it 3.386 r_angle_other_deg 2.982 r_mcangle_it 2.792 r_mcbond_it 2.132 r_rigid_bond_restr 2.022 r_angle_refined_deg 1.973 r_symmetry_vdw_other 0.315 r_nbd_other 0.292 r_metal_ion_refined 0.28 r_nbd_refined 0.229 r_xyhbond_nbd_refined 0.197 r_symmetry_hbond_refined 0.187 r_symmetry_vdw_refined 0.167 r_chiral_restr 0.134 r_nbtor_other 0.104 r_bond_refined_d 0.022 r_gen_planes_refined 0.011 r_gen_planes_other 0.008 r_bond_other_d 0.001 r_nbtor_refined r_xyhbond_nbd_other r_metal_ion_other r_symmetry_hbond_other r_mcbond_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5596 Nucleic Acid Atoms Solvent Atoms 1025 Heterogen Atoms 6
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling