3FGY | pdb_00003fgy

CRYSTAL STRUCTURE OF A NTF2-LIKE PROTEIN (BXE_B1094) FROM BURKHOLDERIA XENOVORANS LB400 AT 1.59 A RESOLUTION

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	10.5	277	30.0000% PEG-400, 0.1M CAPS pH 10.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.31	46.64

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 45.95	α = 90
b = 66.08	β = 90
c = 91	γ = 90

Symmetry
Space Group	P 21 21 21

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 300 mm CCD	Adjustable focusing mirrors in K-B geometry	2008-10-11	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-B	0.94645,0.97967	APS	23-ID-B

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	1.59	29.037	99	0.044	14.92	4.6		37939		-3	20.169

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	1.59	1.65	99.4		0.446	1.7

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	1.59	29.037	37883	1890	99.69	0.184	0.183	0.19	0.211	0.21	RANDOM	23.121

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]
0.67			0.09		-0.76

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.782
r_dihedral_angle_4_deg	15.995
r_dihedral_angle_3_deg	13.872
r_dihedral_angle_1_deg	5.683
r_scangle_it	5.554
r_scbond_it	4.22
r_mcangle_it	2.62
r_mcbond_it	1.952
r_angle_refined_deg	1.553
r_angle_other_deg	0.949
r_mcbond_other	0.47
r_symmetry_vdw_other	0.346
r_nbd_refined	0.212
r_nbd_other	0.208
r_symmetry_vdw_refined	0.202
r_nbtor_refined	0.172
r_symmetry_hbond_refined	0.155
r_xyhbond_nbd_refined	0.147
r_chiral_restr	0.089
r_nbtor_other	0.088
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	2028
Nucleic Acid Atoms
Solvent Atoms	329
Heterogen Atoms	26

Software

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