4XM1

N,N'-diacetylchitobiose deacetylase from Pyrococcus furiosus in the presence of cadmium


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP82980.1M Tris-HCl (pH 8.0), 0.2M MgCl2, 3.2M 1,6-hexanediol, 5mM CdCl2
Crystal Properties
Matthews coefficientSolvent content
2.3347.32

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 74.353α = 66.39
b = 77.847β = 84.7
c = 93.511γ = 61.95
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX300HE2013-10-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL44XU0.9SPring-8BL44XU

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
11.85097.710.43.6152603
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)
11.81.8695.80.3992.63.2

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONTHROUGHOUT1.841.13144947765697.620.240760.238140.2902RANDOM39.105
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]
0.10.060.160.01-0.450.16
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.829
r_dihedral_angle_4_deg18.694
r_dihedral_angle_3_deg16.548
r_dihedral_angle_1_deg6.339
r_scangle_it3.926
r_scbond_it3.153
r_angle_refined_deg1.907
r_mcangle_it1.873
r_mcbond_it1.174
r_chiral_restr0.126
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.829
r_dihedral_angle_4_deg18.694
r_dihedral_angle_3_deg16.548
r_dihedral_angle_1_deg6.339
r_scangle_it3.926
r_scbond_it3.153
r_angle_refined_deg1.907
r_mcangle_it1.873
r_mcbond_it1.174
r_chiral_restr0.126
r_bond_refined_d0.022
r_gen_planes_refined0.01
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 Atoms12914
Nucleic Acid Atoms
Solvent Atoms362
Heterogen Atoms74

Software

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