4R6K | pdb_00004r6k

Crystal structure of ABC transporter substrate-binding protein YesO from Bacillus subtilis, TARGET EFI-510761, an open conformation

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2DVU

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7.5		Protein: 10 mM BIS-TRIS, 500 mm NaCl, 5% glycerol, 5 mm DTT; reservoir: 1.4 m sodium citrate, 0.1 m HEPES-NaOH, pH 7.5; vapor diffusion, sitting drop, temperature 294K

Crystal Properties
Matthews coefficient	Solvent content
2.09	41.22

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 44.932	α = 90
b = 75.727	β = 90
c = 119.738	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	MIRRORS	2014-06-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X29A		NSLS	X29A

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	1.94	50	99.3	0.079	0.079	25	6.9		30836		-5

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	1.94	1.97	94.2		0.78	0.78	1.7	5.7

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	MR	THROUGHOUT	2DVU	1.94	50	29819	952	99.11	0.19383	0.1918	0.2	0.25981	0.27	RANDOM	39.652

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]
2.17			-2.18		0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.849
r_dihedral_angle_4_deg	20.309
r_dihedral_angle_3_deg	15.893
r_scangle_other	13.727
r_long_range_B_other	13.719
r_long_range_B_refined	13.656
r_scbond_it	13.434
r_scbond_other	13.434
r_mcangle_other	7.64
r_mcangle_it	7.638
r_mcbond_it	7.528
r_mcbond_other	7.517
r_dihedral_angle_1_deg	5.524
r_angle_refined_deg	1.376
r_angle_other_deg	0.791
r_chiral_restr	0.088
r_bond_refined_d	0.01
r_gen_planes_refined	0.007
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3179
Nucleic Acid Atoms
Solvent Atoms	202
Heterogen Atoms	1

Software

Software
Software Name	Purpose
PHASER	phasing
ARP/wARP	model building
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling