1W1K

STRUCTURE OF THE OCTAMERIC FLAVOENZYME VANILLYL-ALCOHOL OXIDASE: Ile238Thr Mutant


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2VAOPDB ENTRY 2VAO

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
14.6FROM 6% PEG4000, 100 MM ACETATE BUFFER PH 4.6
Crystal Properties
Matthews coefficientSolvent content
2.340

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 129.896α = 90
b = 129.896β = 90
c = 133.383γ = 90
Symmetry
Space GroupI 4

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMARRESEARCHMIRRORS2002-11-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM14ESRFBM14

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
12.553098.90.1012.233857

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 2VAO2.554033857177898.90.210.2070.272RANDOM46.57
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]
-1.88-1.883.77
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.993
r_scangle_it2.628
r_scbond_it1.665
r_angle_refined_deg1.523
r_mcangle_it1.058
r_mcbond_it0.561
r_nbd_refined0.224
r_symmetry_vdw_refined0.218
r_xyhbond_nbd_refined0.161
r_chiral_restr0.102
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.993
r_scangle_it2.628
r_scbond_it1.665
r_angle_refined_deg1.523
r_mcangle_it1.058
r_mcbond_it0.561
r_nbd_refined0.224
r_symmetry_vdw_refined0.218
r_xyhbond_nbd_refined0.161
r_chiral_restr0.102
r_symmetry_hbond_refined0.056
r_bond_refined_d0.015
r_gen_planes_refined0.005
r_bond_other_d
r_angle_other_deg
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_gen_planes_other
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
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8700
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms128

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
CCP4phasing