2QEU

Crystal structure of putative carboxymuconolactone decarboxylase (YP_555818.1) from Burkholderia xenovorans LB400 at 1.65 A resolution

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.57	277	NANODROP, 23.4% PEG 4000, 15.0% Glycerol, 0.17M Ammonium acetate, 0.1M Citric acid pH 5.57, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.52	51.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 71.173	α = 90
b = 71.173	β = 90
c = 325.501	γ = 120

Symmetry
Space Group	P 61 2 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	2007-06-03	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2	0.91837, 0.97903, 0.97920	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	1.65	29.761	100	0.147	0.147	13.8	10.6		60310			17.94

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	1.65	1.69	100		0.012	1.24	2	10.8	4353

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	1.65	29.761	60156	3039	99.97	0.154	0.152	0.18	RANDOM	9.037

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]
0.51	0.25		0.51		-0.76

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.898
r_dihedral_angle_4_deg	15.408
r_dihedral_angle_3_deg	11.702
r_scangle_it	7.126
r_dihedral_angle_1_deg	5.428
r_scbond_it	4.947
r_mcangle_it	2.477
r_mcbond_it	1.873
r_angle_refined_deg	1.764
r_angle_other_deg	1.054
r_mcbond_other	0.511
r_symmetry_vdw_refined	0.353
r_symmetry_vdw_other	0.28
r_nbd_refined	0.235
r_symmetry_hbond_refined	0.195
r_xyhbond_nbd_refined	0.194
r_nbd_other	0.19
r_nbtor_refined	0.182
r_chiral_restr	0.1
r_nbtor_other	0.085
r_xyhbond_nbd_other	0.059
r_bond_refined_d	0.017
r_gen_planes_refined	0.007
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3025
Nucleic Acid Atoms
Solvent Atoms	410
Heterogen Atoms	91

Software

Software
Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
SCALA	data scaling
PDB_EXTRACT	data extraction
MAR345	data collection
MOSFLM	data reduction
SHELXD	phasing
SOLVE	phasing