2DRW

The crystal structutre of D-amino acid amidase from Ochrobactrum anthropi SV3

X-RAY DIFFRACTION

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Crystallization

Crystal Properties
Matthews coefficient	Solvent content
2.21	44.43

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 77.205	α = 90
b = 123.219	β = 104.36
c = 115.706	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		2005-05-22	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL38B1	0.9791, 0.9793, 0.9900	SPring-8	BL38B1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.1	47.57	99.2				117625		1

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.1	2.18	91.8

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	MAD	THROUGHOUT	2.1	47.57	115879	6124	99.92	0.18526	0.18217	0.24321	RANDOM	26.864

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.395
r_dihedral_angle_4_deg	18.841
r_dihedral_angle_3_deg	15.02
r_dihedral_angle_1_deg	6.398
r_scangle_it	2.428
r_scbond_it	1.571
r_angle_refined_deg	1.265
r_mcangle_it	1.054
r_mcbond_it	0.574
r_nbtor_refined	0.302
r_metal_ion_refined	0.248
r_nbd_refined	0.201
r_symmetry_vdw_refined	0.197
r_symmetry_hbond_refined	0.191
r_xyhbond_nbd_refined	0.161
r_chiral_restr	0.086
r_bond_refined_d	0.01
r_gen_planes_refined	0.004
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_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	16380
Nucleic Acid Atoms
Solvent Atoms	2056
Heterogen Atoms	23

Software

Software
Software Name	Purpose
REFMAC	refinement
JUPITOR210	data reduction
HKL-2000	data scaling
SHELXD	phasing