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Structure of Pseudomonas cellulosa alpha-D-glucuronidase complexed with glucuronic acid and xylotriose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other NATIVE ALPHA-D-GLUCURONIDASE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8 30MG/ML, 15% PEG3350, 250MM MGCL2, 5MM TRIS PH8.0, 20% ETHYLENE GLYCOL, 50MM GLUCURONIC ACID, 50MM XYLOTRIOSE, pH 8.00
Crystal Properties Matthews coefficient Solvent content 2.4 47.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.256 α = 115.15 b = 74.323 β = 92.94 c = 87.273 γ = 109.24
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 110 IMAGE PLATE MARRESEARCH OSMICS CONFOCAL MULTILAYER 2001-08-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RUH3R
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 1.67 20 93.9 0.049 15.7 2.7 159491
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 1.67 1.7 86.4 0.225 3 2.5
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT NATIVE ALPHA-D-GLUCURONIDASE 1.67 20 156986 1256 94.1 0.146 0.146 0.172 0.2063 RANDOM 14.57
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] 0.84 -0.05 -0.27 -0.69 -0.48 -0.61
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.145 r_dihedral_angle_1_deg 5.738 r_scangle_it 3.657 r_scbond_it 2.339 r_angle_other_deg 1.971 r_angle_refined_deg 1.724 r_mcangle_it 1.44 r_mcbond_it 0.813 r_nbd_refined 0.211 r_symmetry_vdw_other 0.187
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.145 r_dihedral_angle_1_deg 5.738 r_scangle_it 3.657 r_scbond_it 2.339 r_angle_other_deg 1.971 r_angle_refined_deg 1.724 r_mcangle_it 1.44 r_mcbond_it 0.813 r_nbd_refined 0.211 r_symmetry_vdw_other 0.187 r_nbd_other 0.158 r_symmetry_vdw_refined 0.148 r_symmetry_hbond_refined 0.123 r_chiral_restr 0.122 r_xyhbond_nbd_refined 0.106 r_nbtor_other 0.094 r_bond_refined_d 0.016 r_gen_planes_refined 0.009 r_bond_other_d 0.004 r_gen_planes_other 0.004 r_dihedral_angle_2_deg r_dihedral_angle_4_deg r_nbtor_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_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 11262 Nucleic Acid Atoms Solvent Atoms 1422 Heterogen Atoms 100
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling