2E82 | pdb_00002e82

Crystal structure of human D-amino acid oxidase complexed with imino-DOPA


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2DU8PDB ENTRY 2DU8

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP829310% PEG 4000, 0.1M SODIUM CITRATE, 0.2M AMMONIUM ACETATE, 10% GLYCEROL, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.243.98

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 150.015α = 90
b = 181.886β = 90
c = 50.916γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU JUPITER 2102006-12-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL26B11.0SPring-8BL26B1

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
12.74097.50.06814.6638354
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)
2.72.892.20.2075.53546

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 2DU82.74036386191897.530.212230.212230.209930.210.254330.25RANDOM37.139
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]
-1.95-1.693.64
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.875
r_dihedral_angle_4_deg21.667
r_dihedral_angle_3_deg17.964
r_dihedral_angle_1_deg5.276
r_scangle_it2.373
r_angle_refined_deg1.497
r_scbond_it1.406
r_mcangle_it1.367
r_mcbond_it0.765
r_nbtor_refined0.317
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.875
r_dihedral_angle_4_deg21.667
r_dihedral_angle_3_deg17.964
r_dihedral_angle_1_deg5.276
r_scangle_it2.373
r_angle_refined_deg1.497
r_scbond_it1.406
r_mcangle_it1.367
r_mcbond_it0.765
r_nbtor_refined0.317
r_nbd_refined0.231
r_symmetry_hbond_refined0.208
r_symmetry_vdw_refined0.184
r_xyhbond_nbd_refined0.16
r_chiral_restr0.083
r_bond_refined_d0.012
r_gen_planes_refined0.004
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 Atoms10932
Nucleic Acid Atoms
Solvent Atoms126
Heterogen Atoms268

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing