2DNS

The crystal structure of D-amino acid amidase from Ochrobactrum anthropi SV3 complexed with D-Phenylalanine

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2D83	PDB entry, 2D83

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.9	293	pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.22	44.69

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 77.067	α = 90
b = 123.702	β = 104.44
c = 116.046	γ = 90

Symmetry
Space Group	P 1 21 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	CCD	RIGAKU JUPITER 210		2005-07-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL38B1	1.0	SPring-8	BL38B1

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)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	2.4	50	99.9	0.11	0.099			80647	80614		1

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)
	2.4	2.49	99.6		0.486	0.434

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry, 2D83	2.4	19.87	77883	77883	4106	99.56	0.19917	0.19917	0.19548	0.26873	RANDOM	31.24

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]
-0.01		-0.01	0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.831
r_dihedral_angle_4_deg	19.833
r_dihedral_angle_3_deg	16.349
r_dihedral_angle_1_deg	6.393
r_scangle_it	1.906
r_angle_refined_deg	1.262
r_scbond_it	1.186
r_mcangle_it	0.871
r_metal_ion_refined	0.561
r_mcbond_it	0.472

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.831
r_dihedral_angle_4_deg	19.833
r_dihedral_angle_3_deg	16.349
r_dihedral_angle_1_deg	6.393
r_scangle_it	1.906
r_angle_refined_deg	1.262
r_scbond_it	1.186
r_mcangle_it	0.871
r_metal_ion_refined	0.561
r_mcbond_it	0.472
r_nbtor_refined	0.3
r_nbd_refined	0.202
r_symmetry_vdw_refined	0.199
r_symmetry_hbond_refined	0.192
r_xyhbond_nbd_refined	0.154
r_chiral_restr	0.083
r_bond_refined_d	0.009
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	16274
Nucleic Acid Atoms
Solvent Atoms	745
Heterogen Atoms	75

Software

Software
Software Name	Purpose
REFMAC	refinement
JUPITOR210	data reduction
DENZO	data reduction
SCALEPACK	data scaling
MLPHARE	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.