3G9X

Structure of haloalkane dehalogenase DhaA14 mutant I135F from Rhodococcus rhodochrous


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
19277[protein]=7-10 mg/ml in 50mM Tris-HCl buffer pH 7.5; [Precipitant]=25% PEG 4000, 8% 2-propanol in 100mM sodium acetate., VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.1440.94

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42.73α = 115.5
b = 44.44β = 97.87
c = 46.63γ = 109.52
Symmetry
Space GroupP 1

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 X11EMBL/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
10.953094.20.0590.05926.45.81634957.9
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)
10.950.9790.60.4180.4184.44

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 1BN60.9510163371163371817994.20.11490.11490.11490.1374RANDOM8.763
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]
0.140.140.410.030.30.3
Coordinate Error
Structure Solution MethodRefinement High ResolutionRefinement Low Resolution
642132.72881.55
RMS Deviations
KeyRefinement Restraint Deviation
s_zero_chiral_vol0.104
s_non_zero_chiral_vol0.1
s_anti_bump_dis_restr0.036
s_similar_adp_cmpnt0.033
s_angle_d0.031
s_from_restr_planes0.0283
s_bond_d0.015
s_rigid_bond_adp_cmpnt0.005
s_similar_dist
s_approx_iso_adps
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2372
Nucleic Acid Atoms
Solvent Atoms520
Heterogen Atoms9

Software

Software
Software NamePurpose
SHELXL-97refinement
MOLREPphasing
REFMACrefinement
Cootmodel building
MolProbitymodel building
DENZOdata reduction
SCALEPACKdata scaling
HKL-2000data collection