5EUM | pdb_00005eum

1.8 Angstrom Crystal Structure of ATP-binding Component of Fused Lipid Transporter Subunits of ABC superfamily from Haemophilus influenzae.

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	295	Protein: 8.5 mg/ml, 0.01M Tris-HCL (pH 8.3); Screen: JCSG+ (E2), 0.2M Sodium chloride, 0.1M Sodium cacodylate (pH 6.5), 2M Ammonium sulfate; Cryo: 1:1 (screen solution) : (50% Sucrose).

Crystal Properties
Matthews coefficient	Solvent content
2.39	48.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 95.237	α = 90
b = 95.237	β = 90
c = 60.87	γ = 90

Symmetry
Space Group	P 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 300 mm CCD		2015-10-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-G	0.98756	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	1.8	30	99.8	0.048	0.048	32.8	7.5		50720		-3	35.2

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	1.8	1.83	100		0.64	3.4	7.5

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	2GHI	1.8	29.46	47918	2598	99.73	0.1727	0.17104	0.18	0.20394	0.22	RANDOM	42.179

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]
-0.45			-0.45		0.91

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.33
r_dihedral_angle_4_deg	11.27
r_dihedral_angle_3_deg	9.72
r_long_range_B_refined	7.527
r_long_range_B_other	7.455
r_scangle_other	3.686
r_dihedral_angle_1_deg	3.162
r_mcangle_it	2.524
r_mcangle_other	2.524
r_scbond_it	2.366
r_scbond_other	2.366
r_mcbond_it	1.639
r_mcbond_other	1.626
r_angle_refined_deg	1.405
r_angle_other_deg	0.85
r_chiral_restr	0.092
r_gen_planes_refined	0.022
r_gen_planes_other	0.018
r_bond_refined_d	0.009
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	3871
Nucleic Acid Atoms
Solvent Atoms	305
Heterogen Atoms	117

Software

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