1GQK

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


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 100MM GLUCURONIC ACID, pH 8.00
Crystal Properties
Matthews coefficientSolvent content
2.447.8

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 69.707α = 115.34
b = 74.879β = 93.06
c = 87.481γ = 109.2
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
11.92097.30.0829.82.5113754
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)
11.91.9394.10.3532.22.4

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-GLUCURONIDASE1.919.7311180786997.30.1520.1510.186RANDOM16.67
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]
1.260.53-0.10.02-0.53-1.4
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg15.88
r_dihedral_angle_1_deg4.301
r_scangle_it3.398
r_scbond_it2.238
r_angle_other_deg1.812
r_angle_refined_deg1.485
r_mcangle_it1.335
r_mcbond_it0.799
r_nbtor_other0.244
r_nbd_refined0.224
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg15.88
r_dihedral_angle_1_deg4.301
r_scangle_it3.398
r_scbond_it2.238
r_angle_other_deg1.812
r_angle_refined_deg1.485
r_mcangle_it1.335
r_mcbond_it0.799
r_nbtor_other0.244
r_nbd_refined0.224
r_nbd_other0.195
r_symmetry_vdw_other0.192
r_symmetry_vdw_refined0.156
r_xyhbond_nbd_refined0.119
r_chiral_restr0.108
r_symmetry_hbond_refined0.083
r_xyhbond_nbd_other0.069
r_bond_refined_d0.016
r_gen_planes_refined0.008
r_gen_planes_other0.004
r_bond_other_d0.002
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 AtomsNumber
Protein Atoms11376
Nucleic Acid Atoms
Solvent Atoms1285
Heterogen Atoms82

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling