2DU8

Crystal structure of human D-amino acid oxidase

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1AN9	PDB ENTRY 1AN9

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	288	10% PEG 4000, 0.2M ammonium acetate, 0.1M sodium citrate, 12% glycerol, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 288.0K

Crystal Properties
Matthews coefficient	Solvent content
2.23	44.91

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 150.976	α = 90
b = 183.184	β = 90
c = 51.075	γ = 90

Symmetry
Space Group	P 21 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	ADSC QUANTUM 315		2006-05-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-5A	1.0	Photon Factory	BL-5A

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	2.5	116.25	99.5	0.077	13.4	5.8		49644

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)
	2.5	2.59	99.8		0.377		5.5

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 1AN9	2.5	46.78	47032	2516	99.08	0.22535	0.22296	0.27006	RANDOM	51.856

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]
3.37			-1.64		-1.73

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.564
r_dihedral_angle_4_deg	17.747
r_dihedral_angle_3_deg	17.464
r_angle_other_deg	13.385
r_dihedral_angle_1_deg	5.14
r_scangle_it	3.039
r_scbond_it	2.215
r_mcangle_it	1.552
r_angle_refined_deg	1.384
r_mcbond_it	1.052
r_nbtor_refined	0.313
r_nbtor_other	0.29
r_nbd_refined	0.222
r_symmetry_vdw_refined	0.185
r_symmetry_hbond_refined	0.153
r_xyhbond_nbd_refined	0.144
r_mcbond_other	0.136
r_bond_other_d	0.105
r_chiral_restr	0.083
r_gen_planes_other	0.079
r_bond_refined_d	0.012
r_gen_planes_refined	0.006
r_nbd_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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10932
Nucleic Acid Atoms
Solvent Atoms	256
Heterogen Atoms	248

Software

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