3EBT | pdb_00003ebt

Crystal structure of a ntf2-like protein of unknown function (bpss0132) from burkholderia pseudomallei k96243 at 1.30 A resolution

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		277	20.0000% Glycerol, 0.0400M KH2PO4, 16.0000% PEG-8000, No Buffer pH None, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.74	55.12

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 75.73	α = 90
b = 75.73	β = 90
c = 50.07	γ = 120

Symmetry
Space Group	P 31 2 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)	2008-08-01	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1	0.91837,0.97848,0.97904	SSRL	BL11-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	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	1.3	27.431	99	0.062	0.078	9.59			40949		-3	13.652

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.3	1.35	98.2		0.481	0.607	2.1

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	1.3	27.431	40924	2061	99.77	0.141	0.14	0.1488	0.162	0.1707	RANDOM	20.271

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]
-0.36	-0.18		-0.36		0.55

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.561
r_dihedral_angle_4_deg	12.502
r_dihedral_angle_3_deg	10.642
r_sphericity_free	8.015
r_sphericity_bonded	5.733
r_dihedral_angle_1_deg	4.916
r_scangle_it	4.905
r_scbond_it	3.943
r_rigid_bond_restr	3.077
r_mcangle_it	2.95
r_mcbond_it	2.254
r_angle_refined_deg	1.76
r_mcbond_other	1.61
r_angle_other_deg	1.519
r_symmetry_vdw_other	0.267
r_nbd_refined	0.211
r_symmetry_vdw_refined	0.186
r_nbd_other	0.18
r_nbtor_refined	0.169
r_xyhbond_nbd_refined	0.124
r_chiral_restr	0.111
r_symmetry_hbond_refined	0.101
r_nbtor_other	0.078
r_bond_refined_d	0.017
r_gen_planes_refined	0.009
r_bond_other_d	0.007
r_gen_planes_other	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1032
Nucleic Acid Atoms
Solvent Atoms	209
Heterogen Atoms	12

Software

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