4K3F | pdb_00004k3f

Crystal structure of a putative TonB-dependent receptor (PA5505) from Pseudomonas aeruginosa PAO1 at 1.60 A resolution

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	293	3.20M ammonium sulfate, 0.7% n-Butanol, 0.1M HEPES pH 7.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.34	47.41

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 99.577	α = 90
b = 40.509	β = 90
c = 60.813	γ = 90

Symmetry
Space Group	P 21 21 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	PIXEL	DECTRIS PILATUS 6M	Rhodium-coated vertical and horizontal focusing mirrors; liquid-nitrogen cooled double crystal Si(111) monochromator	2013-04-01	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL12-2	0.8265,0.9794,0.9792	SSRL	BL12-2

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	1.6	29.135	92.4	0.056	9.16			32359		-3	19.747

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	1.6	1.66	92.1		0.467	1.9

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	1.6	29.135	32319	1641	97.07	0.1523	0.1506	0.16	0.1847	0.19	RANDOM	22.2558

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]
0.95			-0.68		-0.28

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	42.163
r_dihedral_angle_4_deg	15.994
r_dihedral_angle_3_deg	13.063
r_dihedral_angle_1_deg	5.903
r_mcangle_it	2.415
r_mcbond_other	1.827
r_mcbond_it	1.826
r_angle_refined_deg	1.536
r_angle_other_deg	0.812
r_chiral_restr	0.097

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	42.163
r_dihedral_angle_4_deg	15.994
r_dihedral_angle_3_deg	13.063
r_dihedral_angle_1_deg	5.903
r_mcangle_it	2.415
r_mcbond_other	1.827
r_mcbond_it	1.826
r_angle_refined_deg	1.536
r_angle_other_deg	0.812
r_chiral_restr	0.097
r_bond_refined_d	0.012
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1832
Nucleic Acid Atoms
Solvent Atoms	257
Heterogen Atoms	50

Software

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.