4XLZ

N,N'-diacetylchitobiose deacetylase (SeMet derivative) from Pyrococcus furiosus in the presence of cadmium


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3WL4 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP82980.1M Tris-HCl (pH 8.0), 0.2M MgCl2, 3.0M 1,6-hexanediol, 5mM CdCl2
Crystal Properties
Matthews coefficientSolvent content
4.0469.59

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 93.895α = 74.69
b = 93.88β = 74.68
c = 93.877γ = 74.68
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152013-10-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL38B10.99522SPring-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
11.515095.215.81.9435340

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 REPLACEMENTTHROUGHOUT3WL41.5131.164134842185295.650.15260.151830.16714RANDOM21.222
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]
-0.010.010.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.845
r_dihedral_angle_4_deg18.022
r_dihedral_angle_3_deg12.683
r_scangle_it6.314
r_dihedral_angle_1_deg5.907
r_scbond_it4.034
r_angle_refined_deg2.911
r_mcangle_it2.606
r_mcbond_it1.595
r_chiral_restr0.214
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.845
r_dihedral_angle_4_deg18.022
r_dihedral_angle_3_deg12.683
r_scangle_it6.314
r_dihedral_angle_1_deg5.907
r_scbond_it4.034
r_angle_refined_deg2.911
r_mcangle_it2.606
r_mcbond_it1.595
r_chiral_restr0.214
r_bond_refined_d0.035
r_gen_planes_refined0.017
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 Atoms13140
Nucleic Acid Atoms
Solvent Atoms1412
Heterogen Atoms466

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing