3BTP | pdb_00003btp

Crystal structure of Agrobacterium tumefaciens VirE2 in complex with its chaperone VirE1: a novel fold and implications for DNA binding

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	MICROBATCH UNDER OIL	7	292	20% PEG 6000, 0.2M NH4Cl, 1% Triton X-405, pH 7.0, MICROBATCH UNDER OIL, temperature 292K

Crystal Properties
Matthews coefficient	Solvent content
1.96	37.14

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 51.02	α = 90
b = 96.271	β = 90
c = 112.483	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	ADSC QUANTUM 315	Single Silicon (111) monochromator and toroidal focusing mirror	2006-12-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-4	0.97900, 0.98000, 0.97600	ESRF	ID14-4

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	2.3	50	99.8	0.109	0.099	16.8	7.1		23980

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	2.3	2.38	99.9		0.386	0.403	4.6	6.6

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	SAD	THROUGHOUT	2.3	48.14	23872	23873	1288	99.55	0.21178	0.20931	0.21	0.25576	0.25	RANDOM	32.3

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]
-0.75			0.22		0.54

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.973
r_dihedral_angle_4_deg	21.046
r_dihedral_angle_3_deg	18.404
r_dihedral_angle_1_deg	8.409
r_scangle_it	5.266
r_scbond_it	3.44
r_angle_refined_deg	2.26
r_mcangle_it	2.251
r_mcbond_it	1.45
r_nbtor_refined	0.308
r_nbd_refined	0.24
r_symmetry_vdw_refined	0.216
r_chiral_restr	0.186
r_xyhbond_nbd_refined	0.167
r_symmetry_hbond_refined	0.076
r_bond_refined_d	0.025
r_gen_planes_refined	0.009
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3380
Nucleic Acid Atoms
Solvent Atoms	71
Heterogen Atoms	10

Software

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