4F5Z

Crystal structure of Rhodococcus rhodochrous haloalkane dehalogenase mutant (L95V, A172V).


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3FBWPDB entry 3FBW

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.527935 % (w/v) PEG4000, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 279K
Crystal Properties
Matthews coefficientSolvent content
2.0640.43

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42.663α = 115.28
b = 44.489β = 98.61
c = 46.389γ = 109.55
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2012-01-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.20.978BESSY14.2

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
11.25091.70.03518.852.6784557.6
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)
11.21.2472.10.1912.51.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONFOURIER SYNTHESISTHROUGHOUTPDB entry 3FBW1.217.1774518393791.630.121850.121850.120070.15495RANDOM14.122
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]
0.190.090.170.230.19-0.14
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.803
r_dihedral_angle_4_deg18.44
r_dihedral_angle_3_deg12.094
r_dihedral_angle_1_deg5.773
r_sphericity_free5.659
r_sphericity_bonded4.208
r_scangle_it3.365
r_scbond_it2.57
r_mcangle_it1.819
r_rigid_bond_restr1.777
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.803
r_dihedral_angle_4_deg18.44
r_dihedral_angle_3_deg12.094
r_dihedral_angle_1_deg5.773
r_sphericity_free5.659
r_sphericity_bonded4.208
r_scangle_it3.365
r_scbond_it2.57
r_mcangle_it1.819
r_rigid_bond_restr1.777
r_angle_refined_deg1.531
r_mcbond_it1.296
r_nbtor_refined0.323
r_nbd_refined0.211
r_symmetry_vdw_refined0.171
r_symmetry_hbond_refined0.163
r_xyhbond_nbd_refined0.16
r_chiral_restr0.1
r_bond_refined_d0.012
r_gen_planes_refined0.009
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2350
Nucleic Acid Atoms
Solvent Atoms745
Heterogen Atoms10

Software

Software
Software NamePurpose
MarDBdata collection
MOLREPphasing
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling