4URF

Molecular Genetic and Crystal Structural Analysis of 1-(4- Hydroxyphenyl)-Ethanol Dehydrogenase from Aromatoleum aromaticum EbN1


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4UREPDB ENTRY 4URE

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROPSITTING DROP METHOD IN A BUFFER CONTAINING 30% PEG 6000, 0.1 M NA-CACODYLATE (PH 6.5), 0.3 M MG-ACETATE
Crystal Properties
Matthews coefficientSolvent content
1.9737.48

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 121.5α = 90
b = 55.1β = 134.4
c = 86.3γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUSMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06DASLSX06DA

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
11.131.896.70.0814.52.5160008
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)
11.11.290.10.3811.342.3

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 4URE1.131.77152002800197.060.110110.108890.13309RANDOM11.201
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]
0.280.21-0.12-0.2
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free66.379
r_dihedral_angle_2_deg35.554
r_dihedral_angle_4_deg16.897
r_sphericity_bonded15.281
r_dihedral_angle_3_deg12.21
r_dihedral_angle_1_deg6.233
r_scbond_it6.222
r_rigid_bond_restr5.666
r_angle_refined_deg2.082
r_mcangle_it1.684
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free66.379
r_dihedral_angle_2_deg35.554
r_dihedral_angle_4_deg16.897
r_sphericity_bonded15.281
r_dihedral_angle_3_deg12.21
r_dihedral_angle_1_deg6.233
r_scbond_it6.222
r_rigid_bond_restr5.666
r_angle_refined_deg2.082
r_mcangle_it1.684
r_mcbond_it1.37
r_mcbond_other1.355
r_angle_other_deg0.961
r_chiral_restr0.137
r_bond_refined_d0.021
r_gen_planes_refined0.012
r_bond_other_d0.006
r_gen_planes_other0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3694
Nucleic Acid Atoms
Solvent Atoms490
Heterogen Atoms152

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing