3CUK

Crystal structure of human D-amino acid oxidase: bound to an inhibitor


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.829815% PEG 3350, 0.15M POTASSIUM TRICITR TRIS-HCL, pH 7.80, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.2144.38

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 187.729α = 90
b = 51.145β = 110.45
c = 153.294γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATE2005-02-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRON

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
12.495096.80.097112.946710
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)
12.492.5995.40.55822.9

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 1VE92.4942.5244300236296.480.243420.238930.3285RANDOM23.324
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]
-1.561.04-0.753.04
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.537
r_dihedral_angle_3_deg21.765
r_dihedral_angle_4_deg20.678
r_dihedral_angle_1_deg8.53
r_scangle_it4.235
r_scbond_it2.827
r_angle_refined_deg2.665
r_mcangle_it1.757
r_mcbond_it1.065
r_nbtor_refined0.331
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.537
r_dihedral_angle_3_deg21.765
r_dihedral_angle_4_deg20.678
r_dihedral_angle_1_deg8.53
r_scangle_it4.235
r_scbond_it2.827
r_angle_refined_deg2.665
r_mcangle_it1.757
r_mcbond_it1.065
r_nbtor_refined0.331
r_nbd_refined0.275
r_symmetry_hbond_refined0.206
r_symmetry_vdw_refined0.199
r_xyhbond_nbd_refined0.188
r_chiral_restr0.156
r_bond_refined_d0.028
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms10552
Nucleic Acid Atoms
Solvent Atoms42
Heterogen Atoms256

Software

Software
Software NamePurpose
MOLREPphasing
REFMACrefinement
HKL-2000data scaling