3WL4

N,N'-diacetylchitobiose deacetylase (Se-derivative) from Pyrococcus furiosus


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP82930.1M Tris-HCl (pH 8.0), 0.2M MgCl2, 3.4M 1,6-hexanediol, 5mM CdCl2, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
469.22

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 113.894α = 90
b = 113.894β = 90
c = 201.029γ = 120
Symmetry
Space GroupH 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315rMMAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL38B10.99522, 0.97910, 0.97949SPring-8BL38B1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.545099.814709014352655
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.541.57100

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONMADTHROUGHOUT1.5426.4136328136328719799.850.154390.153620.16888RANDOM22.158
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.832
r_dihedral_angle_4_deg17.339
r_dihedral_angle_3_deg11.918
r_scangle_it6.529
r_dihedral_angle_1_deg6.051
r_scbond_it4.56
r_angle_refined_deg3.254
r_mcangle_it2.605
r_mcbond_it1.749
r_chiral_restr0.35
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.832
r_dihedral_angle_4_deg17.339
r_dihedral_angle_3_deg11.918
r_scangle_it6.529
r_dihedral_angle_1_deg6.051
r_scbond_it4.56
r_angle_refined_deg3.254
r_mcangle_it2.605
r_mcbond_it1.749
r_chiral_restr0.35
r_bond_refined_d0.04
r_gen_planes_refined0.018
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_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 Atoms4380
Nucleic Acid Atoms
Solvent Atoms321
Heterogen Atoms240

Software

Software
Software NamePurpose
HKL-2000data collection
SOLVEphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling