3UK0 | pdb_00003uk0

RPD_1889 protein, an extracellular ligand-binding receptor from Rhodopseudomonas palustris.

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.4	289	0.2 M magnesium sulfate, 20% PEG-4000, 10% glycerol, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
2.07	40.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 43.272	α = 90
b = 71.578	β = 90
c = 105.002	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		2011-04-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.9792	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	1.49	42.3	98.3	0.099	10.3	13.1	53560	53560			27.4

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	1.49	1.52	82.2		0.638	2.07	6.7	2201

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	1.49	42.3	53356	53356	2698	97.82	0.1391	0.1391	0.1361	0.1431	0.1944	0.1973	RANDOM	27.1515

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]
-1.17			2.38		-1.21

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.624
r_sphericity_free	27.716
r_dihedral_angle_4_deg	17.747
r_sphericity_bonded	15.749
r_dihedral_angle_3_deg	14.95
r_dihedral_angle_1_deg	5.544
r_rigid_bond_restr	4.291
r_angle_refined_deg	1.648
r_angle_other_deg	0.986
r_chiral_restr	0.096

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.624
r_sphericity_free	27.716
r_dihedral_angle_4_deg	17.747
r_sphericity_bonded	15.749
r_dihedral_angle_3_deg	14.95
r_dihedral_angle_1_deg	5.544
r_rigid_bond_restr	4.291
r_angle_refined_deg	1.648
r_angle_other_deg	0.986
r_chiral_restr	0.096
r_bond_refined_d	0.015
r_gen_planes_refined	0.009
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2716
Nucleic Acid Atoms
Solvent Atoms	268
Heterogen Atoms	31

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
SHELXD	phasing
MLPHARE	phasing
DM	phasing
SOLVE	phasing
RESOLVE	phasing
HKL-3000	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.