2IPB | pdb_00002ipb

Crystal structure of T159D mutant of S. Typhimurium PhoN protein

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2A96	PDB entry 2A96

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	293	15% PEG-6000, 25mM potassium chloride, 5mM magnesium sulphate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.15	42.66

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 190.273	α = 90
b = 45.113	β = 112.05
c = 112.945	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	293	IMAGE PLATE	MARRESEARCH	mirrors	2005-10-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU200HB	1.5418

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	2.21	30	95.6	0.079	12.7	2.8	43054	43054			28.9

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)
	2.21	2.33	75.8		0.182	4.7	2.6	4944

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	FOURIER SYNTHESIS	THROUGHOUT	PDB entry 2A96	2.23	20	40837	40837	2167	100	0.154	0.154	0.151	0.15	0.208	0.21	RANDOM	29.06

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]
-1.74	0.63	1.43		0.43

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.462
r_dihedral_angle_4_deg	18.83
r_dihedral_angle_3_deg	16.062
r_dihedral_angle_1_deg	6.421
r_scangle_it	3.448
r_mcangle_it	3.102
r_scbond_it	2.251
r_mcbond_it	2.029
r_angle_refined_deg	0.929
r_nbtor_refined	0.319
r_nbd_refined	0.22
r_symmetry_vdw_refined	0.212
r_xyhbond_nbd_refined	0.196
r_symmetry_hbond_refined	0.134
r_chiral_restr	0.081
r_gen_planes_refined	0.01
r_bond_refined_d	0.008
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	7012
Nucleic Acid Atoms
Solvent Atoms	293
Heterogen Atoms

Software

Software
Software Name	Purpose
MAR345dtb	data collection
CCP4	model building
REFMAC	refinement
MAR345	data collection
MOSFLM	data reduction
CCP4	data scaling
CCP4	phasing