4F60

Crystal structure of Rhodococcus rhodochrous haloalkane dehalogenase mutant (T148L, G171Q, A172V, C176F).


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.52770.1M BisTris propane pH6.5, 0.2M Sodium Fluoride,20% PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.2745.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 52.018α = 90
b = 69.93β = 90
c = 85.352γ = 90
Symmetry
Space GroupP 21 21 21

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
11.455095.90.03365.846.9560805378117.6
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)
11.451.574.20.2583.24.8

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 3FBW1.4529.025322350998272195.820.151080.151080.150.17109RANDOM28.683
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]
0.81-0.14-0.66
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.438
r_dihedral_angle_4_deg19.896
r_dihedral_angle_3_deg11.636
r_dihedral_angle_1_deg5.484
r_scangle_it2.677
r_scbond_it1.745
r_angle_refined_deg1.467
r_mcangle_it1.09
r_mcbond_it0.754
r_nbtor_refined0.321
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.438
r_dihedral_angle_4_deg19.896
r_dihedral_angle_3_deg11.636
r_dihedral_angle_1_deg5.484
r_scangle_it2.677
r_scbond_it1.745
r_angle_refined_deg1.467
r_mcangle_it1.09
r_mcbond_it0.754
r_nbtor_refined0.321
r_symmetry_hbond_refined0.221
r_nbd_refined0.209
r_xyhbond_nbd_refined0.152
r_symmetry_vdw_refined0.15
r_chiral_restr0.096
r_bond_refined_d0.012
r_gen_planes_refined0.008
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
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2342
Nucleic Acid Atoms
Solvent Atoms500
Heterogen Atoms1

Software

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