3VNZ

Crystal structure of beta-glucuronidase from Acidobacterium capsulatum in complex with D-glucuronic acid


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3VNYPDB ENTRY 3VNY

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2932.0M sodium phosphate monobasic monohydrate/potassium phosphate dibasic (0.5/9.5 [v/v]), VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.6753.88

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 101.271α = 90
b = 101.271β = 90
c = 217.768γ = 90
Symmetry
Space GroupI 41 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray95CCDADSC QUANTUM 2702010-01-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE AR-NE3A1.0000Photon FactoryAR-NE3A

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
11.840.0199.90.06151.7145264219.8
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)
11.81.831000.29110.4142594

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 REPLACEMENTTHROUGHOUTPDB ENTRY 3VNY1.838.4249797267699.650.200540.198940.23015RANDOM21.954
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]
0.10.1-0.2
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.11
r_dihedral_angle_4_deg14.883
r_dihedral_angle_3_deg13.434
r_dihedral_angle_1_deg5.982
r_scangle_it3.203
r_scbond_it1.969
r_angle_refined_deg1.251
r_mcangle_it1.161
r_mcbond_it0.673
r_chiral_restr0.086
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.11
r_dihedral_angle_4_deg14.883
r_dihedral_angle_3_deg13.434
r_dihedral_angle_1_deg5.982
r_scangle_it3.203
r_scbond_it1.969
r_angle_refined_deg1.251
r_mcangle_it1.161
r_mcbond_it0.673
r_chiral_restr0.086
r_bond_refined_d0.011
r_gen_planes_refined0.006
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3531
Nucleic Acid Atoms
Solvent Atoms349
Heterogen Atoms24

Software

Software
Software NamePurpose
ADSCdata collection
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing