2VNG

Family 51 carbohydrate binding module from a family 98 glycoside hydrolase produced by Clostridium perfringens in complex with blood group A-trisaccharide ligand.


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.5pH 7.5
Crystal Properties
Matthews coefficientSolvent content
1.7942.26

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 69.683α = 90
b = 98.754β = 90
c = 49.241γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray113IMAGE PLATERIGAKU IMAGE PLATEOSMIC BLUEMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-002

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
11.456.889.30.0318.13.41578072
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.41.4368.8

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 DIFFRACTIONOTHERTHROUGHOUTNONE1.456.857807307989.30.1870.1840.235RANDOM13.18
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]
0.830.11-0.93
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.101
r_dihedral_angle_4_deg22.875
r_dihedral_angle_3_deg11.687
r_dihedral_angle_1_deg7.142
r_scangle_it4.926
r_scbond_it4.018
r_mcangle_it2.913
r_mcbond_it2.256
r_angle_refined_deg1.881
r_angle_other_deg0.978
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.101
r_dihedral_angle_4_deg22.875
r_dihedral_angle_3_deg11.687
r_dihedral_angle_1_deg7.142
r_scangle_it4.926
r_scbond_it4.018
r_mcangle_it2.913
r_mcbond_it2.256
r_angle_refined_deg1.881
r_angle_other_deg0.978
r_symmetry_vdw_refined0.371
r_symmetry_vdw_other0.358
r_nbd_refined0.259
r_symmetry_hbond_refined0.244
r_nbd_other0.202
r_nbtor_refined0.182
r_xyhbond_nbd_refined0.166
r_chiral_restr0.121
r_nbtor_other0.094
r_bond_refined_d0.022
r_gen_planes_refined0.01
r_bond_other_d0.001
r_gen_planes_other0.001
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 Atoms2652
Nucleic Acid Atoms
Solvent Atoms585
Heterogen Atoms74

Software

Software
Software NamePurpose
REFMACrefinement
CrystalCleardata reduction
d*TREKdata scaling