1GQL

Structure of Pseudomonas cellulosa alpha-D-glucuronidase complexed with glucuronic acid and xylotriose


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelOtherNATIVE ALPHA-D-GLUCURONIDASE

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1830MG/ML, 15% PEG3350, 250MM MGCL2, 5MM TRIS PH8.0, 20% ETHYLENE GLYCOL, 50MM GLUCURONIC ACID, 50MM XYLOTRIOSE, pH 8.00
Crystal Properties
Matthews coefficientSolvent content
2.447.8

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 69.256α = 115.15
b = 74.323β = 92.94
c = 87.273γ = 109.24
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110IMAGE PLATEMARRESEARCHOSMICS CONFOCAL MULTILAYER2001-08-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RUH3R

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.672093.90.04915.72.7159491
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.671.786.40.22532.5

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTNATIVE ALPHA-D-GLUCURONIDASE1.6720156986125694.10.1460.1460.172RANDOM14.57
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
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg16.145
r_dihedral_angle_1_deg5.738
r_scangle_it3.657
r_scbond_it2.339
r_angle_other_deg1.971
r_angle_refined_deg1.724
r_mcangle_it1.44
r_mcbond_it0.813
r_nbd_refined0.211
r_symmetry_vdw_other0.187
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg16.145
r_dihedral_angle_1_deg5.738
r_scangle_it3.657
r_scbond_it2.339
r_angle_other_deg1.971
r_angle_refined_deg1.724
r_mcangle_it1.44
r_mcbond_it0.813
r_nbd_refined0.211
r_symmetry_vdw_other0.187
r_nbd_other0.158
r_symmetry_vdw_refined0.148
r_symmetry_hbond_refined0.123
r_chiral_restr0.122
r_xyhbond_nbd_refined0.106
r_nbtor_other0.094
r_bond_refined_d0.016
r_gen_planes_refined0.009
r_bond_other_d0.004
r_gen_planes_other0.004
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 AtomsNumber
Protein Atoms11262
Nucleic Acid Atoms
Solvent Atoms1422
Heterogen Atoms100

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling