7ATR | pdb_00007atr

The Crystal Structure of YejA - an ABC Peptide Transporter Receptor

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4ONY

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	291	Protein: 20 mg.ml-1 in 20 mM Tris-HCl, 50 mM NaCl, pH 8.0 Reservoir solution: 2% w/v polyethylene glycol 20,000, 0.1 M 2-(N-morpholino)ethanesulfonic acid, pH 6.5 Drops: 300 nl (150 nl protein solution + 150 nl reservoir solution) Reservoir: 100 microlitres

Crystal Properties
Matthews coefficient	Solvent content
2.57	52.1

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 91.44	α = 90
b = 105.267	β = 90
c = 145.387	γ = 90

Symmetry
Space Group	I 2 2 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS PILATUS3 S 6M		2017-05-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.92819	Diamond	I04

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	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	1.55	85.264	99.6	0.07	0.08	0.038	0.997	14.1	8.4		101011			15.46

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.55	1.58			0.668	0.756	0.353	0.904	2.4	8.5

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	4ONY	1.55	85.264	101009	4874	99.528	0.171	0.1701	0.18	0.1846	0.2	20.793

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]
1.846			-0.539		-1.307

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.24
r_dihedral_angle_4_deg	17.618
r_dihedral_angle_3_deg	12.952
r_dihedral_angle_1_deg	6.791
r_lrange_it	5.839
r_lrange_other	5.749
r_scangle_it	4.862
r_scangle_other	4.862
r_scbond_it	3.283
r_scbond_other	3.282
r_mcangle_it	2.639
r_mcangle_other	2.638
r_mcbond_it	1.863
r_mcbond_other	1.839
r_angle_refined_deg	1.827
r_angle_other_deg	1.455
r_symmetry_xyhbond_nbd_refined	0.632
r_nbd_other	0.283
r_nbd_refined	0.203
r_symmetry_nbd_other	0.181
r_nbtor_refined	0.173
r_symmetry_nbd_refined	0.173
r_xyhbond_nbd_refined	0.168
r_symmetry_xyhbond_nbd_other	0.149
r_chiral_restr	0.097
r_symmetry_nbtor_other	0.081
r_bond_refined_d	0.013
r_gen_planes_refined	0.011
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4841
Nucleic Acid Atoms
Solvent Atoms	408
Heterogen Atoms	18

Software

Software
Software Name	Purpose
REFMAC	refinement
xia2	data processing
Aimless	data reduction
Aimless	data scaling
MOLREP	phasing