3FBW

Structure of Rhodococcus rhodochrous haloalkane dehalogenase DhaA mutant C176Y


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP92940.08M bicine, 8% PEG 8000, 0.08M magnesium chloride, pH 9.0, VAPOR DIFFUSION, SITTING DROP, temperature 294K
Crystal Properties
Matthews coefficientSolvent content
2.2244.54

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42.678α = 90
b = 76.294β = 90
c = 93.098γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mm2007-08-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE X110.8158EMBL/DESY, HAMBURGX11

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
11.231001000.0560.05625.67.48881488814-9999.2
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.231.2599.90.5810.5814.25.74384

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 REPLACEMENTFREE RPDB ENTRY 1BN61.231008873188731342599.90.13690.13690.13640.167RANDOM13.4
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]
Coordinate Error
Structure Solution MethodRefinement High ResolutionRefinement Low Resolution
612267.92738.52
RMS Deviations
KeyRefinement Restraint Deviation
s_zero_chiral_vol0.08
s_non_zero_chiral_vol0.076
s_similar_adp_cmpnt0.036
s_approx_iso_adps0.031
s_angle_d0.028
s_from_restr_planes0.0268
s_anti_bump_dis_restr0.024
s_bond_d0.011
s_rigid_bond_adp_cmpnt0.004
s_similar_dist
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2355
Nucleic Acid Atoms
Solvent Atoms454
Heterogen Atoms17

Software

Software
Software NamePurpose
MAR345data collection
MOLREPphasing
SHELXL-97refinement
HKL-2000data reduction
HKL-2000data scaling