1W1M

STRUCTURE OF THE OCTAMERIC FLAVOENZYME VANILLYL-ALCOHOL OXIDASE: Glu502Gly 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 = 129.906α = 90
b = 129.906β = 90
c = 134.427γ = 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
133097.90.1272.120676
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)
133.1595.40.3232

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 2VAO34020676111397.50.2210.2170.307RANDOM52.5
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]
-1.71-1.713.42
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg7.423
r_scangle_it2.57
r_angle_refined_deg1.671
r_scbond_it1.513
r_mcangle_it1.07
r_mcbond_it0.558
r_nbd_refined0.257
r_symmetry_vdw_refined0.219
r_symmetry_hbond_refined0.183
r_xyhbond_nbd_refined0.18
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg7.423
r_scangle_it2.57
r_angle_refined_deg1.671
r_scbond_it1.513
r_mcangle_it1.07
r_mcbond_it0.558
r_nbd_refined0.257
r_symmetry_vdw_refined0.219
r_symmetry_hbond_refined0.183
r_xyhbond_nbd_refined0.18
r_chiral_restr0.104
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 Atoms8692
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms128

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
CCP4phasing