4ND9 | pdb_00004nd9

The putative substrate binding domain of ABC-type transporter from Agrobacterium tumefaciens in open conformation

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.2	293	PEG8000 20%, NaCl 0.2M, phosphate-citrate, pH 4.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.42	49.21

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 45.702	α = 90
b = 64.155	β = 90
c = 101.123	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 315r	MIRROR	2010-03-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.97929	APS	19-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	85.5				12333

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.3	2.34	88.1

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	SAD	THROUGHOUT	2.3	50	11658	597	89.01	0.2022	0.19963	0.2	0.25282	0.26	RANDOM	22.94

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]
2.99			-2.55		-0.45

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.725
r_dihedral_angle_4_deg	17.29
r_dihedral_angle_3_deg	14.386
r_dihedral_angle_1_deg	5.057
r_scangle_it	1.847
r_scbond_it	1.119
r_angle_refined_deg	0.961
r_angle_other_deg	0.822
r_mcangle_it	0.636
r_mcbond_it	0.326
r_mcbond_other	0.05
r_chiral_restr	0.049
r_bond_refined_d	0.007
r_gen_planes_refined	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2070
Nucleic Acid Atoms
Solvent Atoms	111
Heterogen Atoms

Software

Software
Software Name	Purpose
HKL-3000	data collection
SHELXS	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling