4H77

Crystal structure of haloalkane dehalogenase LinB from Sphingobium sp. MI1205


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1CV2 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8278100mM Tris-HCl (pH 8.0), 20% (w/v) PEG 4000, 200mM CaCl2, VAPOR DIFFUSION, SITTING DROP, temperature 278K
Crystal Properties
Matthews coefficientSolvent content
1.9637.23

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.404α = 90
b = 72.146β = 90
c = 73.492γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray2008-06-07
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE AR-NW12A1.0000Photon FactoryAR-NW12A

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
11.62036060

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 REPLACEMENTTHROUGHOUT1CV21.62034221179799.90.160260.158630.19101RANDOM8.176
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]
-0.520.070.45
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.247
r_dihedral_angle_4_deg14.098
r_dihedral_angle_3_deg13.328
r_dihedral_angle_1_deg5.445
r_scangle_it2.785
r_scbond_it1.716
r_angle_refined_deg1.371
r_mcangle_it0.974
r_mcbond_it0.81
r_nbtor_refined0.317
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.247
r_dihedral_angle_4_deg14.098
r_dihedral_angle_3_deg13.328
r_dihedral_angle_1_deg5.445
r_scangle_it2.785
r_scbond_it1.716
r_angle_refined_deg1.371
r_mcangle_it0.974
r_mcbond_it0.81
r_nbtor_refined0.317
r_symmetry_vdw_refined0.213
r_symmetry_hbond_refined0.211
r_nbd_refined0.205
r_xyhbond_nbd_refined0.143
r_chiral_restr0.092
r_metal_ion_refined0.076
r_symmetry_metal_ion_refined0.012
r_bond_refined_d0.01
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2332
Nucleic Acid Atoms
Solvent Atoms358
Heterogen Atoms21

Software

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