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Structure of Pseudomonas cellulosa alpha-D-glucuronidase complexed with glucuronic acid
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 100MM GLUCURONIC ACID, pH 8.00
Crystal Properties Matthews coefficient Solvent content 2.4 47.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.707 α = 115.34 b = 74.879 β = 93.06 c = 87.481 γ = 109.2
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 1.9 20 97.3 0.082 9.8 2.5 113754
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 94.1 0.353 2.2 2.4
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 NATIVE ALPHA-D-GLUCURONIDASE 1.9 19.73 111807 869 97.3 0.152 0.151 0.1631 0.186 0.1942 RANDOM 16.67
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] 1.26 0.53 -0.1 0.02 -0.53 -1.4
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.88 r_dihedral_angle_1_deg 4.301 r_scangle_it 3.398 r_scbond_it 2.238 r_angle_other_deg 1.812 r_angle_refined_deg 1.485 r_mcangle_it 1.335 r_mcbond_it 0.799 r_nbtor_other 0.244 r_nbd_refined 0.224
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.88 r_dihedral_angle_1_deg 4.301 r_scangle_it 3.398 r_scbond_it 2.238 r_angle_other_deg 1.812 r_angle_refined_deg 1.485 r_mcangle_it 1.335 r_mcbond_it 0.799 r_nbtor_other 0.244 r_nbd_refined 0.224 r_nbd_other 0.195 r_symmetry_vdw_other 0.192 r_symmetry_vdw_refined 0.156 r_xyhbond_nbd_refined 0.119 r_chiral_restr 0.108 r_symmetry_hbond_refined 0.083 r_xyhbond_nbd_other 0.069 r_bond_refined_d 0.016 r_gen_planes_refined 0.008 r_gen_planes_other 0.004 r_bond_other_d 0.002 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 1285 Heterogen Atoms 82
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling