3GWQ

Crystal structure of a putative d-serine deaminase (bxe_a4060) from burkholderia xenovorans lb400 at 2.00 A resolution

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	293	1.0000M NaCitrate, 0.1M Cacodylate pH 6.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.46	50.1

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 113.637	α = 90
b = 113.637	β = 90
c = 145.92	γ = 90

Symmetry
Space Group	P 41 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	MARMOSAIC 325 mm CCD	Flat collimating mirror, toroid focusing mirror	2009-01-08	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2	0.91837,0.97925	SSRL	BL9-2

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	29.881	99	0.109	0.109	11.1	4.9		64237			25.981

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2	2.05	100		0.695	0.695	1.8	4.9	4742

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	29.881	64159	3250	98.62	0.165	0.163	0.205	RANDOM	30.499

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]
-0.46			-0.46		0.92

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.918
r_dihedral_angle_4_deg	20.801
r_dihedral_angle_3_deg	13.236
r_scangle_it	6.846
r_dihedral_angle_1_deg	5.983
r_scbond_it	4.83
r_mcangle_it	2.74
r_mcbond_it	1.669
r_angle_refined_deg	1.438
r_angle_other_deg	0.956
r_mcbond_other	0.739
r_symmetry_vdw_other	0.27
r_symmetry_vdw_refined	0.228
r_nbd_other	0.205
r_nbd_refined	0.201
r_nbtor_refined	0.175
r_xyhbond_nbd_refined	0.14
r_symmetry_hbond_refined	0.116
r_chiral_restr	0.086
r_nbtor_other	0.085
r_metal_ion_refined	0.068
r_bond_refined_d	0.016
r_gen_planes_refined	0.006
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6218
Nucleic Acid Atoms
Solvent Atoms	471
Heterogen Atoms	25

Software

Software
Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
SCALA	data scaling
PDB_EXTRACT	data extraction
MOSFLM	data reduction
SHELXD	phasing
autoSHARP	phasing