3E02 | pdb_00003e02

Crystal structure of a duf849 family protein (bxe_c0271) from burkholderia xenovorans lb400 at 1.90 A resolution

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6	277	1.0000M K/Na Tartrate, 0.1M MES pH 6.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.89	57.39

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 103.837	α = 90
b = 103.837	β = 90
c = 128.969	γ = 120

Symmetry
Space Group	P 62 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	2008-07-16	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2	0.91162,0.97934,0.97892	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	1.9	29.198	99.5	0.107	0.107		7.1		32785			22.755

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	1.9	1.95	99.7		0.625	0.625	1	7.2	2391

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MAD	THROUGHOUT	1.9	29.198	32757	1663	99.31	0.16	0.158	0.16	0.181	0.19	RANDOM	29.295

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]
0.16	0.08		0.16		-0.25

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.508
r_dihedral_angle_4_deg	11.465
r_dihedral_angle_3_deg	10.441
r_scangle_it	4.608
r_dihedral_angle_1_deg	4.117
r_scbond_it	3.279
r_angle_refined_deg	1.617
r_mcangle_it	1.546
r_angle_other_deg	1.402
r_mcbond_it	1.063
r_nbd_refined	0.181
r_mcbond_other	0.165
r_nbtor_refined	0.156
r_symmetry_vdw_refined	0.155
r_nbd_other	0.146
r_symmetry_vdw_other	0.14
r_symmetry_hbond_refined	0.127
r_chiral_restr	0.099
r_xyhbond_nbd_refined	0.091
r_nbtor_other	0.072
r_bond_refined_d	0.013
r_gen_planes_refined	0.005
r_bond_other_d	0.004
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2379
Nucleic Acid Atoms
Solvent Atoms	311
Heterogen Atoms	41

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