4F06 | pdb_00004f06

Crystal structure of solute binding protein of ABC transporter from Rhodopseudomonas palustris HaA2 RPB_2270 in complex with P-HYDROXYBENZOIC ACID

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	3.5	297	2.0 M Ammonium Sulfate 0.1 M Citric Acid, pH 3.5, VAPOR DIFFUSION, SITTING DROP, temperature 297K

Crystal Properties
Matthews coefficient	Solvent content
2.07	40.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.135	α = 90
b = 61.174	β = 90
c = 130.177	γ = 90

Symmetry
Space Group	P 21 21 21

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 315r		2012-02-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.97929	APS	19-ID

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	1.3	50	97.5	0.1	30.3	6.3	83945	81874		-3

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	1.3	1.32	79.3		0.424	2.24	2.9	3298

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	SAD	THROUGHOUT	1.3	50	81790	81790	4085	97.38	0.1234	0.1234	0.1225	0.1202	0.1426	0.1307	RANDOM	13.5009

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]
-0.29			0.54		-0.25

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.359
r_sphericity_free	28.137
r_dihedral_angle_3_deg	11.81
r_sphericity_bonded	10.65
r_dihedral_angle_4_deg	9.611
r_dihedral_angle_1_deg	6.029
r_rigid_bond_restr	4.211
r_angle_refined_deg	1.716
r_chiral_restr	0.106
r_bond_refined_d	0.015

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.359
r_sphericity_free	28.137
r_dihedral_angle_3_deg	11.81
r_sphericity_bonded	10.65
r_dihedral_angle_4_deg	9.611
r_dihedral_angle_1_deg	6.029
r_rigid_bond_restr	4.211
r_angle_refined_deg	1.716
r_chiral_restr	0.106
r_bond_refined_d	0.015
r_gen_planes_refined	0.011

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2783
Nucleic Acid Atoms
Solvent Atoms	380
Heterogen Atoms	64

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing
MLPHARE	phasing
DM	phasing
SHELXDE	phasing
RESOLVE	phasing
ARP/wARP	model building
Coot	model building

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.