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Structure of Pseudomonas cellulosa alpha-D-glucuronidase complexed with xylobiose
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 VAPOR DIFFUSION, HANGING DROP 8 30MG/ML, 15% PEG3350, 250MM MGCL2, 5MM TRIS PH8.0, 20% ETHYLENE GLYCOL 100MM XYLOTRIOSE, pH 8.00
Crystal Properties Matthews coefficient Solvent content 2.4 47.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.561 α = 115.23 b = 74.609 β = 93.15 c = 87.45 γ = 109.17
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 MSC/RIGAKU FOCUSSING MIRRORS 2001-08-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200
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 1.9 20 95 0.089 9.4 2.5 109005
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 1.9 1.93 93.4 0.397 2.1 2.3
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 1.9 20 108150 830 94.7 0.173 0.172 0.221 0.2309 RANDOM 17.64
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] 1.77 0.29 -0.25 -0.61 -1.02 -1.86
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.234 r_dihedral_angle_1_deg 4.528 r_scangle_it 3.054 r_scbond_it 2.016 r_angle_other_deg 1.771 r_angle_refined_deg 1.561 r_mcangle_it 1.222 r_mcbond_it 0.729 r_nbtor_other 0.456 r_nbd_refined 0.219
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.234 r_dihedral_angle_1_deg 4.528 r_scangle_it 3.054 r_scbond_it 2.016 r_angle_other_deg 1.771 r_angle_refined_deg 1.561 r_mcangle_it 1.222 r_mcbond_it 0.729 r_nbtor_other 0.456 r_nbd_refined 0.219 r_symmetry_vdw_other 0.196 r_nbd_other 0.189 r_symmetry_vdw_refined 0.18 r_chiral_restr 0.144 r_xyhbond_nbd_refined 0.122 r_symmetry_hbond_refined 0.117 r_xyhbond_nbd_other 0.052 r_bond_refined_d 0.015 r_gen_planes_refined 0.007 r_gen_planes_other 0.002 r_bond_other_d 0.001 r_dihedral_angle_2_deg r_dihedral_angle_4_deg r_nbtor_refined 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 11376 Nucleic Acid Atoms Solvent Atoms 1383 Heterogen Atoms 94
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling