2VFV

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


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
1.9937.61

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 105.561α = 90
b = 68.455β = 95.19
c = 57.965γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray1002007-03-15MSINGLE 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
11.719.998.50.0424.93.143108
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)
11.71.897.10.0910.93

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 2VFR1.7219.5140994210898.60.1530.1520.184RANDOM10.08
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]
0.03-0.15-0.070.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.663
r_dihedral_angle_4_deg20.256
r_dihedral_angle_3_deg10.988
r_dihedral_angle_1_deg6.131
r_scangle_it3.062
r_scbond_it1.973
r_angle_refined_deg1.73
r_mcangle_it1.131
r_mcbond_it0.768
r_nbtor_refined0.305
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.663
r_dihedral_angle_4_deg20.256
r_dihedral_angle_3_deg10.988
r_dihedral_angle_1_deg6.131
r_scangle_it3.062
r_scbond_it1.973
r_angle_refined_deg1.73
r_mcangle_it1.131
r_mcbond_it0.768
r_nbtor_refined0.305
r_nbd_refined0.215
r_chiral_restr0.203
r_xyhbond_nbd_refined0.106
r_symmetry_hbond_refined0.106
r_symmetry_vdw_refined0.102
r_bond_refined_d0.015
r_gen_planes_refined0.01
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 Atoms3136
Nucleic Acid Atoms
Solvent Atoms525
Heterogen Atoms58

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
CCP4data scaling
CCP4phasing