3CUK

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

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1VE9	PDB ENTRY 1VE9

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.8	298	15% PEG 3350, 0.15M POTASSIUM TRICITR TRIS-HCL, pH 7.80, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.21	44.38

Crystal Data

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

Symmetry
Space Group	C 1 2 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	IMAGE PLATE			2005-02-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	2.49	50	96.8	0.097	11	2.9		46710

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.49	2.59	95.4		0.558	2	2.9

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1VE9	2.49	42.52	44300	2362	96.48	0.24342	0.23893	0.3285	RANDOM	23.324

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]
-1.56		1.04	-0.75		3.04

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.537
r_dihedral_angle_3_deg	21.765
r_dihedral_angle_4_deg	20.678
r_dihedral_angle_1_deg	8.53
r_scangle_it	4.235
r_scbond_it	2.827
r_angle_refined_deg	2.665
r_mcangle_it	1.757
r_mcbond_it	1.065
r_nbtor_refined	0.331
r_nbd_refined	0.275
r_symmetry_hbond_refined	0.206
r_symmetry_vdw_refined	0.199
r_xyhbond_nbd_refined	0.188
r_chiral_restr	0.156
r_bond_refined_d	0.028
r_gen_planes_refined	0.01
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 Atoms	Number
Protein Atoms	10552
Nucleic Acid Atoms
Solvent Atoms	42
Heterogen Atoms	256

Software

Software
Software Name	Purpose
MOLREP	phasing
REFMAC	refinement
HKL-2000	data scaling