2VFU

Alditol Oxidase from Streptomyces coelicolor A3(2): Complex with Mannitol


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2VFRPDB ENTRY 2VFR

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.5pH 6.5
Crystal Properties
Matthews coefficientSolvent content
2.0539.48

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 106.964α = 90
b = 65.931β = 94.49
c = 58.85γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray1002007-03-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU200

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
11.919.999.90.112.4332193
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)
11.921000.541.92.9

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 2VFR1.919.8730623156799.90.1550.1530.199RANDOM18.11
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]
0.3-0.09-0.22-0.09
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.961
r_dihedral_angle_4_deg21.9
r_dihedral_angle_3_deg13.507
r_dihedral_angle_1_deg6.401
r_scangle_it4.105
r_scbond_it2.569
r_angle_refined_deg1.628
r_mcangle_it1.429
r_mcbond_it0.969
r_nbtor_refined0.302
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.961
r_dihedral_angle_4_deg21.9
r_dihedral_angle_3_deg13.507
r_dihedral_angle_1_deg6.401
r_scangle_it4.105
r_scbond_it2.569
r_angle_refined_deg1.628
r_mcangle_it1.429
r_mcbond_it0.969
r_nbtor_refined0.302
r_nbd_refined0.217
r_symmetry_hbond_refined0.184
r_symmetry_vdw_refined0.176
r_xyhbond_nbd_refined0.153
r_chiral_restr0.109
r_bond_refined_d0.019
r_gen_planes_refined0.008
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
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 Atoms3103
Nucleic Acid Atoms
Solvent Atoms439
Heterogen Atoms65

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
CCP4data scaling
CCP4phasing