3LSR | pdb_00003lsr

Crystal structure of DesT in complex with duplex DNA

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3LSP	PDB Entry 3LSP

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	grown under mineral oil	7	291	ML- 0.1M Mes pH7.0, 9% PEG 20K. Protein sample- 0.3 mM protein, 0.3 mM oligo, 0.3 mM 18:1delta9-CoA. Drop- 2ul ML + 2 ul protein + 0.5 uL 1M ammonium sulfate., grown under mineral oil, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
3.35	63.3

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 79.358	α = 90
b = 79.358	β = 90
c = 145.458	γ = 90

Symmetry
Space Group	I 41

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 225 mm CCD	mirrors	2008-10-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-BM	1.0	APS	22-BM

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	2.5	50	96.1	0.049	0.049	40.4	7	15465	14862

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	MOLECULAR REPLACEMENT	THROUGHOUT	PDB Entry 3LSP	2.55	41.38	13546	709	97.36	0.22926	0.2275	0.2264	0.26477	0.2646	RANDOM	61.408

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]
0.02			0.02		-0.03

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.952
r_dihedral_angle_4_deg	20.94
r_dihedral_angle_3_deg	16.644
r_dihedral_angle_1_deg	5.268
r_scangle_it	2.246
r_angle_refined_deg	1.423
r_mcangle_it	1.385
r_scbond_it	1.304
r_mcbond_it	0.769
r_nbtor_refined	0.304
r_nbd_refined	0.221
r_symmetry_hbond_refined	0.171
r_symmetry_vdw_refined	0.13
r_xyhbond_nbd_refined	0.128
r_chiral_restr	0.081
r_bond_refined_d	0.01
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1470
Nucleic Acid Atoms	548
Solvent Atoms	15
Heterogen Atoms	10

Software

Software
Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling