2OXN

Vibrio cholerae family 3 glycoside hydrolase (NagZ) in complex with PUGNAc


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1TR9 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.829815% PEG 20000, 100mM Bis-Tris, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.1141.8

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 48.734α = 90
b = 67.85β = 90
c = 96.894γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IVMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU2001.54

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
11.755.5699.30.06127.27.13584535787
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)
11.71.7995.50.1678.45.1

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 REPLACEMENTTHROUGHOUT1TR91.755.5635779178399.140.170.1680.199RANDOM8.485
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]
-0.06-0.440.5
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.772
r_dihedral_angle_3_deg11.905
r_dihedral_angle_4_deg11.768
r_dihedral_angle_1_deg5.639
r_scangle_it3.394
r_scbond_it2.397
r_angle_refined_deg1.298
r_mcangle_it1.171
r_mcbond_it1.137
r_angle_other_deg0.905
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.772
r_dihedral_angle_3_deg11.905
r_dihedral_angle_4_deg11.768
r_dihedral_angle_1_deg5.639
r_scangle_it3.394
r_scbond_it2.397
r_angle_refined_deg1.298
r_mcangle_it1.171
r_mcbond_it1.137
r_angle_other_deg0.905
r_symmetry_vdw_other0.321
r_symmetry_vdw_refined0.218
r_nbd_refined0.212
r_mcbond_other0.203
r_nbd_other0.2
r_nbtor_refined0.174
r_symmetry_hbond_refined0.135
r_xyhbond_nbd_refined0.132
r_nbtor_other0.083
r_chiral_restr0.079
r_bond_refined_d0.011
r_gen_planes_refined0.005
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2592
Nucleic Acid Atoms
Solvent Atoms381
Heterogen Atoms25

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
CrystalCleardata collection
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing