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Crystal structure of chondroitin sulfate lyase abc from bacteroides thetaiotaomicron wal2926
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.5 282 17% PEG 3350, 0.2M ammonium sulfate, 100 mM HEPES , pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 282K, pH 6.50
Crystal Properties Matthews coefficient Solvent content 3.44 64.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 223.362 α = 90 b = 223.362 β = 90 c = 112.639 γ = 120
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 MARMOSAIC 300 mm CCD DOUBLE-CRYSTAL FIXED-EXIT SI- 111 MONOCHROMATOR (E/E~10-4) AND A PLANAR PALLADIUM-COATED SILICON MIRROR 2006-05-26 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID APS 22-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.85 50 94.7 0.063 0.05 14.6 3.1 71079
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.85 2.92 56.7 0.4 0.326 1.6 1.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 SAD THROUGHOUT 2.85 50 67482 3599 94.8 0.222 0.22 0.2115 0.262 0.2516 RANDOM 59.33
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] -1.88 -0.94 -1.88 2.82
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.854 r_dihedral_angle_3_deg 17.472 r_dihedral_angle_4_deg 15.287 r_dihedral_angle_1_deg 5.167 r_scangle_it 1.864 r_mcangle_it 1.214 r_scbond_it 1.195 r_angle_refined_deg 1.007 r_mcbond_it 0.826 r_nbtor_refined 0.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.854 r_dihedral_angle_3_deg 17.472 r_dihedral_angle_4_deg 15.287 r_dihedral_angle_1_deg 5.167 r_scangle_it 1.864 r_mcangle_it 1.214 r_scbond_it 1.195 r_angle_refined_deg 1.007 r_mcbond_it 0.826 r_nbtor_refined 0.3 r_nbd_refined 0.189 r_symmetry_vdw_refined 0.179 r_symmetry_hbond_refined 0.176 r_xyhbond_nbd_refined 0.111 r_metal_ion_refined 0.073 r_chiral_restr 0.07 r_bond_refined_d 0.006 r_gen_planes_refined 0.002 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_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 15824 Nucleic Acid Atoms Solvent Atoms 67 Heterogen Atoms 82
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling RESOLVE phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction SHARP phasing