1W1L

STRUCTURE OF THE OCTAMERIC FLAVOENZYME VANILLYL-ALCOHOL OXIDASE: Phe454Tyr 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 = 129.9α = 90
b = 129.9β = 90
c = 133.608γ = 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
12.73097.60.0882.128185
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)
12.72.8594.60.38832

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 2VAO2.74028185150897.60.2080.2030.293RANDOM53.27
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]
-2.35-2.354.71
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg7.36
r_scangle_it2.727
r_scbond_it1.645
r_angle_refined_deg1.567
r_mcangle_it1.046
r_mcbond_it0.547
r_nbd_refined0.236
r_symmetry_hbond_refined0.225
r_symmetry_vdw_refined0.196
r_xyhbond_nbd_refined0.174
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg7.36
r_scangle_it2.727
r_scbond_it1.645
r_angle_refined_deg1.567
r_mcangle_it1.046
r_mcbond_it0.547
r_nbd_refined0.236
r_symmetry_hbond_refined0.225
r_symmetry_vdw_refined0.196
r_xyhbond_nbd_refined0.174
r_chiral_restr0.102
r_bond_refined_d0.014
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 Atoms8704
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms128

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
CCP4phasing