2UVG

Structure of a periplasmic oligogalacturonide binding protein from Yersinia enterocolitica


X-RAY DIFFRACTION

Crystallization

Crystal Properties
Matthews coefficientSolvent content
2.0444.8

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 43.978α = 90
b = 79.523β = 90
c = 117.772γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray113 MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODE

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
12.22096.20.0810.43.58208103

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT2.265.9419725107595.90.1960.1920.265RANDOM22.66
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]
0.95-0.47-0.48
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.415
r_dihedral_angle_4_deg26.845
r_dihedral_angle_3_deg17.282
r_dihedral_angle_1_deg11.253
r_scangle_it4.129
r_scbond_it2.873
r_angle_refined_deg1.933
r_mcangle_it1.636
r_mcbond_it1.074
r_symmetry_vdw_refined0.561
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.415
r_dihedral_angle_4_deg26.845
r_dihedral_angle_3_deg17.282
r_dihedral_angle_1_deg11.253
r_scangle_it4.129
r_scbond_it2.873
r_angle_refined_deg1.933
r_mcangle_it1.636
r_mcbond_it1.074
r_symmetry_vdw_refined0.561
r_symmetry_hbond_refined0.35
r_nbtor_refined0.313
r_nbd_refined0.264
r_xyhbond_nbd_refined0.207
r_chiral_restr0.192
r_bond_refined_d0.022
r_gen_planes_refined0.009
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_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 Atoms3219
Nucleic Acid Atoms
Solvent Atoms376
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement