3FWH

Structure of haloalkane dehalogenase mutant Dha15 (I135F/C176Y) from Rhodococcus rhodochrous


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1BN6PDB ENTRY 1BN6

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.527725 % PEG 4 000, 8 % iso-propanol and 100 mM Na-Acetate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.0540.05

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42.524α = 115.48
b = 44.37β = 98.41
c = 46.541γ = 109.6
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 345 mm plateMIRROR: ELLIPTICALLY BENT 12 QUARTZ SEGMENTSMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE X11EMBL/DESY, HAMBURGX11

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
11.22090.70.0529.63.477114111.1
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)
11.21.24450.1796.82.1

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 REPLACEMENTTHROUGHOUTPDB ENTRY 1BN61.222077113387294.40.1320.130.162RANDOM8.817
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]
0.510.340.12-0.080.1-0.08
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.902
r_dihedral_angle_4_deg21.933
r_dihedral_angle_3_deg14.245
r_sphericity_free8.381
r_dihedral_angle_1_deg5.863
r_sphericity_bonded4.293
r_scangle_it3.789
r_scbond_it2.731
r_mcangle_it2.058
r_mcbond_other2.025
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.902
r_dihedral_angle_4_deg21.933
r_dihedral_angle_3_deg14.245
r_sphericity_free8.381
r_dihedral_angle_1_deg5.863
r_sphericity_bonded4.293
r_scangle_it3.789
r_scbond_it2.731
r_mcangle_it2.058
r_mcbond_other2.025
r_angle_refined_deg1.605
r_rigid_bond_restr1.517
r_mcbond_it1.433
r_angle_other_deg0.974
r_symmetry_hbond_refined0.242
r_symmetry_vdw_refined0.204
r_xyhbond_nbd_refined0.168
r_chiral_restr0.102
r_bond_refined_d0.014
r_gen_planes_refined0.011
r_gen_planes_other0.003
r_bond_other_d0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
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
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2393
Nucleic Acid Atoms
Solvent Atoms617
Heterogen Atoms10

Software

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