3GSM

Vibrio cholerae family 3 glycoside hydrolase (NagZ) bound to N-Valeryl-PUGNAc


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.229813% PEG 20,000, 10% glycerol, 100mM Bis-Tris pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.3848.24

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 47.98α = 90
b = 86.44β = 90
c = 86.44γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV++2008-10-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RUH2R1.54

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
12.461.0899.50.16.72.971460914482
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)
12.42.531000.492.23

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2OXN2.461.08153351375572799.140.21250.209370.27174RANDOM26.499
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]
0.1-1.321.21
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.705
r_dihedral_angle_4_deg19.779
r_dihedral_angle_3_deg17.257
r_dihedral_angle_1_deg5.893
r_scangle_it2.499
r_scbond_it1.461
r_angle_refined_deg1.311
r_mcangle_it0.991
r_angle_other_deg0.632
r_mcbond_it0.523
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.705
r_dihedral_angle_4_deg19.779
r_dihedral_angle_3_deg17.257
r_dihedral_angle_1_deg5.893
r_scangle_it2.499
r_scbond_it1.461
r_angle_refined_deg1.311
r_mcangle_it0.991
r_angle_other_deg0.632
r_mcbond_it0.523
r_mcbond_other0.091
r_chiral_restr0.065
r_bond_refined_d0.011
r_gen_planes_refined0.005
r_bond_other_d
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2512
Nucleic Acid Atoms
Solvent Atoms128
Heterogen Atoms30

Software

Software
Software NamePurpose
CrystalCleardata collection
PHASERphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling