4NF0 | pdb_00004nf0

CRYSTAL STRUCTURE OF A TRAP PERIPLASMIC SOLUTE BINDING PROTEIN FROM PSEUDOMONAS AERUGINOSA PAO1 (PA4616), TARGET EFI-510182, WITH BOUND L-Malate

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4MX6	pdb entry 4MX6

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	sitting drop vapor diffusion	7.5	298	Protein (10 mg/ml, 10 mM HEPES pH 7.5, 5 mM DTT, 10 mM DL-Malate); Reservoir (0.2 M Ammonium Sulfate, 22%(w/v) PEG 4000, 0.1 M Sodium Acetate); Cryoprotection (20% ethylene glycol, 80% 2.0 M reservoir), sitting drop vapor diffusion, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.11	41.63

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 71.959	α = 99.01
b = 73.91	β = 91.59
c = 122.14	γ = 95.09

Symmetry
Space Group	P 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	RAYONIX MX225HE	MIRRORS	2013-08-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 31-ID	0.9793	APS	31-ID

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	1.85	120.525	96.7	0.075	0.075	5.4	4.1	204171	204171			22.62

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)
1	1.85	1.87	95.3		0.73	0.73	4.2	3.9	38804

Refinement

Statistics
Diffraction ID	Structure Solution Method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	pdb entry 4MX6	1.85	33.563	202871	202871	10206	96.08	0.1969	0.1947	0.19	0.2391	0.24	RANDOM	31.6144

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]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	13.795
f_angle_d	1.041
f_chiral_restr	0.043
f_bond_d	0.007
f_plane_restr	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	17411
Nucleic Acid Atoms
Solvent Atoms	1654
Heterogen Atoms	93

Software

Software
Software Name	Purpose
SCALA	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction
AMoRE	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.