4HZG

Structure of haloalkane dehalogenase DhaA from Rhodococcus rhodochrous


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.7527739% PEG 4000, 100 mM sodium acetate, 8% 1,2,3-trichloropropane, pH 7.75, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.141.31

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42.77α = 115.27
b = 44.47β = 97.77
c = 46.51γ = 109.23
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX-2252011-10-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.21.9BESSY14.2

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
11.852287.80.1585.33.7238432093420.45
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)
11.851.9481.50.56823.43508

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 3FBW1.9522191501701792388.860.218570.218570.215580.27287RANDOM19.533
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]
2.41.190.9-0.34-0.03-1.43
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.725
r_dihedral_angle_4_deg21.464
r_dihedral_angle_3_deg15.801
r_dihedral_angle_1_deg6.523
r_angle_refined_deg1.665
r_angle_other_deg0.92
r_chiral_restr0.092
r_bond_refined_d0.014
r_gen_planes_refined0.009
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.725
r_dihedral_angle_4_deg21.464
r_dihedral_angle_3_deg15.801
r_dihedral_angle_1_deg6.523
r_angle_refined_deg1.665
r_angle_other_deg0.92
r_chiral_restr0.092
r_bond_refined_d0.014
r_gen_planes_refined0.009
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2368
Nucleic Acid Atoms
Solvent Atoms226
Heterogen Atoms1

Software

Software
Software NamePurpose
MAR345data collection
MOLREPphasing
REFMACrefinement
XDSdata reduction
SCALAdata scaling