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CRYSTAL STRUCTURE OF CHONDROITINASE B COMPLEXED TO DERMATAN SULFATE HEXASACCHARIDE
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1DBG PDB ENTRY 1DBG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8.7 PEG8000, 2-METHYL-2,4- PENTADIOL, AMMONIUM ACETATE, TRIS, pH 8.70
Crystal Properties Matthews coefficient Solvent content 1.95 34.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.574 α = 90 b = 73.989 β = 93.93 c = 59.063 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 CCD 2000-11-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X8C NSLS X8C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.7 34.98 92.5 0.041 16.5 2.85 44254
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.7 1.76 65.3 0.149 5.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1DBG 1.7 40 42015 2211 92.5 0.135 0.133 0.1353 0.176 0.1791 RANDOM 13.47
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] 0.02 -0.25 -0.02 -0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.783 r_dihedral_angle_4_deg 16.062 r_dihedral_angle_3_deg 12.615 r_dihedral_angle_1_deg 6.922 r_scangle_it 4.312 r_scbond_it 2.789 r_angle_refined_deg 1.839 r_mcangle_it 1.725 r_mcbond_it 1.013 r_nbd_refined 0.227
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.783 r_dihedral_angle_4_deg 16.062 r_dihedral_angle_3_deg 12.615 r_dihedral_angle_1_deg 6.922 r_scangle_it 4.312 r_scbond_it 2.789 r_angle_refined_deg 1.839 r_mcangle_it 1.725 r_mcbond_it 1.013 r_nbd_refined 0.227 r_symmetry_vdw_refined 0.214 r_xyhbond_nbd_refined 0.158 r_symmetry_hbond_refined 0.146 r_chiral_restr 0.14 r_metal_ion_refined 0.081 r_bond_refined_d 0.019 r_gen_planes_refined 0.009 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_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3784 Nucleic Acid Atoms Solvent Atoms 757 Heterogen Atoms 196
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling CNS phasing