3Q16

Linkage between the Bacterial Acid Stress and Stringent Responses: The Structure of the Inducible Lysine Decarboxylase

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3N75	PDB ENTRY 3N75

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	285	0.1 M Tris, 0.1 M ammonium bromide, 25-35% PEG1000, 0-10% glycerol, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 285K

Crystal Properties
Matthews coefficient	Solvent content
4.18	70.55

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 270.29	α = 90
b = 181.29	β = 125.06
c = 169.93	γ = 90

Symmetry
Space Group	C 1 2 1

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	MAR CCD 130 mm		2009-12-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CLSI BEAMLINE 08ID-1		CLSI	08ID-1

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	4.1	140.227	77.4	0.219	0.219	6.2	2.7	52673	40852

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	4.1	4.32	79.3		0.421	0.421	1.7	2.6

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 3N75	4.1	68	38774	2077	77.58	0.27771	0.27629	0.28	0.30432	0.3	RANDOM	100.395

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]
3.45		-2.94	-0.01		-6.82

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.809
r_dihedral_angle_3_deg	13.396
r_dihedral_angle_4_deg	8.446
r_dihedral_angle_1_deg	3.429
r_angle_refined_deg	0.766
r_nbtor_refined	0.293
r_mcangle_it	0.191
r_nbd_refined	0.152
r_scangle_it	0.131
r_symmetry_vdw_refined	0.126
r_symmetry_hbond_refined	0.118
r_mcbond_it	0.107
r_xyhbond_nbd_refined	0.096
r_scbond_it	0.069
r_chiral_restr	0.046
r_bond_refined_d	0.005
r_gen_planes_refined	0.003
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	28485
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
MxDC	data collection
MOSFLM	data reduction
SCALA	data scaling
REFMAC	phasing