2Q0T

Crystal structure of a putative gamma-carboxymuconolactone decarboxylase subunit (bxe_b0980) from burkholderia xenovorans lb400 at 1.70 A resolution

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	277	NANODROP, 20.0% PEG 8000, 0.1M HEPES pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.3	46.42

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 50.3	α = 90
b = 83.11	β = 103.16
c = 99.26	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	MARMOSAIC 325 mm CCD	Flat mirror (vertical focusing)	2007-05-04	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1	0.91162, 0.97941, 0.97905	SSRL	BL11-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	1.7	29.086	95	0.074	6.95			86578		-3	16.23

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)
1	1.7	1.76	93.6		0.492	1.4

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	1.7	29.086	86554	4333	98.99	0.156	0.154	0.193	RANDOM	13.832

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]
0.09		0.3	0.18		-0.13

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.085
r_dihedral_angle_4_deg	16.522
r_dihedral_angle_3_deg	12.462
r_scangle_it	6.327
r_dihedral_angle_1_deg	4.988
r_scbond_it	4.525
r_mcangle_it	2.575
r_mcbond_it	2.115
r_angle_refined_deg	1.509
r_angle_other_deg	1.07
r_mcbond_other	0.57
r_nbd_refined	0.225
r_nbd_other	0.195
r_symmetry_vdw_other	0.189
r_nbtor_refined	0.176
r_xyhbond_nbd_refined	0.17
r_symmetry_vdw_refined	0.159
r_symmetry_hbond_refined	0.145
r_chiral_restr	0.094
r_nbtor_other	0.084
r_bond_refined_d	0.017
r_gen_planes_refined	0.007
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5908
Nucleic Acid Atoms
Solvent Atoms	943
Heterogen Atoms

Software

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