3E49 | pdb_00003e49

Crystal structure of a prokaryotic domain of unknown function (duf849) with a tim barrel fold (bxe_c0966) from burkholderia xenovorans lb400 at 1.75 A resolution

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	277	40.0000% 2-ethoxyethanol, 0.0500M Ca(OAc)2, 0.1M Imidazole pH 8.0, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K, VAPOR DIFFUSION, SITTING DROP

Crystal Properties
Matthews coefficient	Solvent content
2.22	44.55

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 59.495	α = 69.99
b = 68.275	β = 88.07
c = 83.952	γ = 72.84

Symmetry
Space Group	P 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 collimating mirror, toroid focusing mirror	2008-07-17	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2	0.91837,0.97936,0.97892	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	1.75	29.656	97.2	0.069	0.069	6.6	2.7		115967			21.904

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)
	1.75	1.8	96		0.444	0.444	1.7	2.7	8444

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	1.75	29.656	115965	5804	97.24	0.179	0.177	0.18	0.218	0.22	RANDOM	24.44

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]
-1.3	1.95	-0.71	1.19	-0.31	-0.77

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.629
r_dihedral_angle_4_deg	13.596
r_dihedral_angle_3_deg	11.904
r_scangle_it	5.541
r_scbond_it	4.211
r_dihedral_angle_1_deg	4.019
r_mcangle_it	2.417
r_angle_refined_deg	1.751
r_mcbond_it	1.68
r_angle_other_deg	1.039
r_mcbond_other	0.321
r_symmetry_vdw_other	0.268
r_nbd_refined	0.215
r_nbd_other	0.207
r_symmetry_vdw_refined	0.197
r_nbtor_refined	0.185
r_symmetry_hbond_refined	0.185
r_xyhbond_nbd_refined	0.179
r_metal_ion_refined	0.142
r_chiral_restr	0.113
r_xyhbond_nbd_other	0.108
r_nbtor_other	0.089
r_bond_refined_d	0.018
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	9355
Nucleic Acid Atoms
Solvent Atoms	946
Heterogen Atoms	79

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