3UKJ | pdb_00003ukj

Crystal structure of extracellular ligand-binding receptor from Rhodopseudomonas palustris HaA2

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	297	10 mM Nickel chloride, 0.1M Tris, 20% PEG2000 MME, 10 mM Praseodymium Acetate, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 297K

Crystal Properties
Matthews coefficient	Solvent content
2	38.63

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.685	α = 90
b = 70.314	β = 90
c = 104.688	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		2011-04-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.97921	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	1.6	50	98.8	0.098	31.9	6.5	42597	42082		-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	1.6	1.63	97.5		0.589	2.46	5.6	2037

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	1.6	50	42032	42032	2127	98.81	0.1609	0.1609	0.1585	0.1623	0.2056	0.2064	RANDOM	18.1433

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]
-1.97			2.2		-0.23

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.204
r_dihedral_angle_4_deg	18.717
r_dihedral_angle_3_deg	11.77
r_dihedral_angle_1_deg	5.345
r_scangle_it	4.69
r_scbond_it	3.252
r_mcangle_it	1.947
r_rigid_bond_restr	1.536
r_angle_refined_deg	1.43
r_mcbond_it	1.249

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.204
r_dihedral_angle_4_deg	18.717
r_dihedral_angle_3_deg	11.77
r_dihedral_angle_1_deg	5.345
r_scangle_it	4.69
r_scbond_it	3.252
r_mcangle_it	1.947
r_rigid_bond_restr	1.536
r_angle_refined_deg	1.43
r_mcbond_it	1.249
r_chiral_restr	0.119
r_gen_planes_refined	0.021
r_bond_refined_d	0.015

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2689
Nucleic Acid Atoms
Solvent Atoms	404
Heterogen Atoms	20

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.