2EFU | pdb_00002efu

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

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2DRW	DAA native structure (2DRW)

Crystallization

Crystal Properties
Matthews coefficient	Solvent content
2.23	44.93

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 77.468	α = 90
b = 123.274	β = 104.05
c = 116.156	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		2005-09-24	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	2.3	50	100	0.093	0.096		6.1		93589

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)
	2.3	2.38	100		0.359

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	DAA native structure (2DRW)	2.3	47.67	89171	4735	99.99	0.17373	0.17047	0.17	0.23524	0.24	RANDOM	25.417

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	34.809
r_dihedral_angle_4_deg	19.608
r_dihedral_angle_3_deg	15.1
r_dihedral_angle_1_deg	6.365
r_scangle_it	2.328
r_scbond_it	1.453
r_angle_refined_deg	1.255
r_mcangle_it	0.975
r_mcbond_it	0.518
r_metal_ion_refined	0.428
r_nbtor_refined	0.301
r_symmetry_metal_ion_refined	0.272
r_nbd_refined	0.199
r_symmetry_vdw_refined	0.194
r_symmetry_hbond_refined	0.155
r_xyhbond_nbd_refined	0.15
r_chiral_restr	0.085
r_bond_refined_d	0.01
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	16410
Nucleic Acid Atoms
Solvent Atoms	1407
Heterogen Atoms	98

Software

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