5ENT

Minocycline bound structure of bacterial efflux pump.

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5EN5

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		291	0.1 M MES pH6.5, 0.21 M NaCl, 11.5% PEG4000

Crystal Properties
Matthews coefficient	Solvent content
2.77	55.65

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 109.557	α = 90
b = 145.409	β = 90
c = 175.612	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	PIXEL	DECTRIS PILATUS 6M		2015-11-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)	0.97625	PETRA III, EMBL c/o DESY	P13 (MX1)

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	2.5	50	99.3	0.162	0.997	11.5	9		96991

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.5	2.59	99.3		1.241	0.617		8.9

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	5EN5	2.5	50	92224	4767	99.86	0.19601	0.19337	0.24768	RANDOM	52.249

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]
1.44			-2.88		1.45

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.008
r_dihedral_angle_4_deg	19.475
r_dihedral_angle_3_deg	15.863
r_long_range_B_other	9.15
r_long_range_B_refined	9.145
r_scangle_other	6.724
r_dihedral_angle_1_deg	6.62
r_mcangle_other	6.078
r_mcangle_it	6.077
r_scbond_it	4.248
r_scbond_other	4.248
r_mcbond_it	3.963
r_mcbond_other	3.949
r_angle_refined_deg	1.655
r_angle_other_deg	0.998
r_chiral_restr	0.087
r_bond_refined_d	0.014
r_gen_planes_refined	0.007
r_bond_other_d	0.002
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	16886
Nucleic Acid Atoms
Solvent Atoms	371
Heterogen Atoms	40

Software

Software
Software Name	Purpose
REFMAC	refinement
xia2	data reduction
XDS	data scaling
PHASER	phasing