5D6A | pdb_00005d6a

2.7 Angstrom Crystal Structure of ABC transporter ATPase from Vibrio vulnificus in Complex with Adenylyl-imidodiphosphate (AMP-PNP)

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5	295	Protein: 5.9 mg/ml, 0.5M Sodium chloride, 0.01M Tris-HCL (pH 8.3), 1mM AMPPNP; Screen: PACT (C2), 0.1M PCB buffer (pH 5.0), 25% (w/v) PEG 1500

Crystal Properties
Matthews coefficient	Solvent content
2.17	43.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 104.957	α = 90
b = 104.957	β = 90
c = 85.354	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 225 mm CCD		2014-11-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-G	0.97856	APS	21-ID-G

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	2.7	30	100	0.117	0.117	32.5	11	15243	15243		-3	57.9

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.7	2.75	100		0.621	5	11.2

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	2.7	28.55	13687	1535	99.8	0.19991	0.1941	0.1985	0.25555	0.2615	RANDOM	55.709

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]
-0.15	-0.08		-0.15		0.5

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	22.501
r_dihedral_angle_4_deg	7.935
r_dihedral_angle_3_deg	7.764
r_long_range_B_refined	4.125
r_long_range_B_other	4.086
r_mcangle_it	2.049
r_mcangle_other	2.049
r_scangle_other	1.928
r_dihedral_angle_1_deg	1.771
r_mcbond_it	1.156
r_mcbond_other	1.155
r_scbond_it	1.147
r_scbond_other	1.147
r_angle_refined_deg	1.051
r_angle_other_deg	0.67
r_chiral_restr	0.062
r_gen_planes_refined	0.019
r_gen_planes_other	0.015
r_bond_refined_d	0.004
r_bond_other_d	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	4297
Nucleic Acid Atoms
Solvent Atoms	84
Heterogen Atoms	32

Software

Software
Software Name	Purpose
REFMAC	refinement
BLU-MAX	data collection
HKL-3000	phasing
HKL-3000	data scaling
PHENIX	phasing