3VSJ

Crystal structure of 1,6-APD (2-ANIMOPHENOL-1,6-DIOXYGENASE) complexed with intermediate products


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3VSGPDB ENTRY 3VSG

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.529825% PEG 3350, 0.2M SODIUM CHLORIDE, PH 6.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K
Crystal Properties
Matthews coefficientSolvent content
2.652.63

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 270.24α = 90
b = 48.39β = 109.57
c = 108.55γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray98IMAGE PLATERIGAKU RAXIS IV++MIRRORS2007-04-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-E SUPERBRIGHT1.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
12.339.8797.760.1090.10915.75.2596095531131
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.32.4286.50.4560.4562.73.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 3VSG2.339.875960955311294797.760.1920.191880.189620.23397RANDOM20.072
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]
-0.19-0.910.32-0.74
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.903
r_dihedral_angle_3_deg15.964
r_dihedral_angle_4_deg14.524
r_dihedral_angle_1_deg5.66
r_scangle_it1.3
r_angle_refined_deg1.033
r_angle_other_deg0.828
r_scbond_it0.752
r_mcangle_it0.56
r_mcbond_it0.291
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.903
r_dihedral_angle_3_deg15.964
r_dihedral_angle_4_deg14.524
r_dihedral_angle_1_deg5.66
r_scangle_it1.3
r_angle_refined_deg1.033
r_angle_other_deg0.828
r_scbond_it0.752
r_mcangle_it0.56
r_mcbond_it0.291
r_chiral_restr0.058
r_mcbond_other0.038
r_gen_planes_refined0.007
r_bond_refined_d0.006
r_gen_planes_other0.004
r_bond_other_d0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8892
Nucleic Acid Atoms
Solvent Atoms1035
Heterogen Atoms23

Software

Software
Software NamePurpose
CrystalCleardata collection
PHASESphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling