5DAJ

Crystal structure of NalD, the secondary repressor of MexAB-OprM multidrug efflux pump in Pseudomonas aeruginosa

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6	289	Tacsimate, Sodium citrate tribasic dihydrate, PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.75	55.36

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 61.639	α = 90
b = 128.137	β = 90
c = 266.063	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	CCD	ADSC QUANTUM 315r		2012-06-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL17U	1.0	SSRF	BL17U

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.65	50	99.6	0.1	17.4	7.4		61847

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	2.65	2.74	99.4		0.8	3.8	7.5

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	2.65	30	58632	3122	99.34	0.21335	0.21048	0.2661	RANDOM	87.04

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]
-4.52			2.23		2.28

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	69.054
r_sphericity_bonded	41.922
r_dihedral_angle_2_deg	33.257
r_dihedral_angle_4_deg	17.337
r_dihedral_angle_3_deg	17.15
r_long_range_B_refined	11.88
r_long_range_B_other	11.759
r_scangle_other	10.254
r_mcangle_it	9.823
r_mcangle_other	9.823
r_scbond_it	7.969
r_scbond_other	7.969
r_mcbond_other	7.287
r_mcbond_it	7.286
r_rigid_bond_restr	5.832
r_dihedral_angle_1_deg	4.734
r_angle_other_deg	1.485
r_angle_refined_deg	1.305
r_chiral_restr	0.069
r_bond_refined_d	0.009
r_bond_other_d	0.006
r_gen_planes_refined	0.005
r_gen_planes_other	0.005
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

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	12585
Nucleic Acid Atoms
Solvent Atoms	10
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing