2IIU | pdb_00002iiu

Crystal structure of a putative PhoU-like phosphate regulatory protein (NP_719307.1) from Shewanella oneidensis MR-1 at 2.28 A resolution.

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP, NANODROP	6.5	277	1.0M NaCitrate, 0.1M Cacodylate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.7	54.08

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 99.88	α = 90
b = 99.88	β = 90
c = 397.27	γ = 120

Symmetry
Space Group	H 3 2

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 315	Flat mirror (vertical focusing)	2006-05-07	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1	0.918370, 0.979318, 0.979035	SSRL	BL11-1

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	46.73	98.5	0.134	14.54	20.2		52278			39.053

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	2.05	100		0.651	2.91

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MAD	THROUGHOUT	2.28	47.458	35397	1812	99.88	0.202	0.2	0.21	0.247	0.25	RANDOM	44.494

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]
2.44	1.22		2.44		-3.66

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.541
r_dihedral_angle_4_deg	12.969
r_dihedral_angle_3_deg	12.594
r_scangle_it	7.449
r_scbond_it	5.242
r_dihedral_angle_1_deg	2.878
r_mcangle_it	2.858
r_mcbond_it	1.826
r_angle_refined_deg	1.509
r_angle_other_deg	0.88
r_mcbond_other	0.372
r_symmetry_vdw_other	0.261
r_symmetry_hbond_refined	0.244
r_nbd_refined	0.228
r_xyhbond_nbd_refined	0.202
r_nbtor_refined	0.184
r_nbd_other	0.159
r_symmetry_vdw_refined	0.158
r_nbtor_other	0.091
r_chiral_restr	0.088
r_bond_refined_d	0.017
r_gen_planes_refined	0.005
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4799
Nucleic Acid Atoms
Solvent Atoms	203
Heterogen Atoms	16

Software

Software
Software Name	Purpose
MolProbity	model building
SHARP	phasing
REFMAC	refinement
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
SHELXD	phasing