4NH2 | pdb_00004nh2

Crystal structure of AmtB from E. coli bound to phosphatidylglycerol

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1U7G	PDB ENTRY 1U7G

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.6	298	15% PEG 4000, 0.8M potassium formate, 0.1M sodium acetate pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.68	54.04

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 116.19	α = 90
b = 201.19	β = 90
c = 232.45	γ = 90

Symmetry
Space Group	C 2 2 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	PIXEL	PSI PILATUS 6M		2013-10-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.97949	Diamond	I04

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	2.3	40	99.4	0.124	13.66			119767	2	-3	40.041

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.3	2.36	96.3		1.204	1.204	2.48

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	PDB ENTRY 1U7G	2.3	38.74	119766	5951	99.3	0.2033	0.2017	0.2055	0.2338	0.2383	RANDOM	45.5591

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]
-32.35			-37.46		69.81

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.824
r_dihedral_angle_4_deg	18.554
r_dihedral_angle_3_deg	13.931
r_mcangle_it	6.121
r_dihedral_angle_1_deg	6.089
r_mcbond_it	4.346
r_mcbond_other	4.346
r_angle_refined_deg	1.67
r_angle_other_deg	1.313
r_chiral_restr	0.095
r_bond_refined_d	0.016
r_gen_planes_refined	0.011
r_bond_other_d	0.008
r_gen_planes_other	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	15856
Nucleic Acid Atoms
Solvent Atoms	111
Heterogen Atoms	293

Software

Software
Software Name	Purpose
XSCALE	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
GDA	data collection
PHASER	phasing