3K3G

Crystal Structure of the Urea Transporter from Desulfovibrio Vulgaris Bound to 1,3-dimethylurea

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	293	23% PEG 1500, 100 mM Na Cacodylate, 10 mM N,N'-dimethylurea, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
4.14	70.29

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 110.106	α = 90
b = 110.106	β = 90
c = 84.872	γ = 120

Symmetry
Space Group	P 63

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 315		2009-06-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 24-ID-E	0.98	APS	24-ID-E

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	2.4	50	99.5	0.091	8.5	10.8		22979

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	2.4	2.44	97.6		0.915		6.8	1138

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	3K3F	2.4	27.47	22964	22964	1166	99.61	0.187	0.187	0.186	0.214	RANDOM	44.871

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]
0.45	0.22		0.45		-0.67

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.846
r_dihedral_angle_4_deg	21.68
r_dihedral_angle_3_deg	15.737
r_dihedral_angle_1_deg	5.49
r_scangle_it	2.101
r_scbond_it	1.468
r_angle_refined_deg	1.338
r_mcangle_it	0.985
r_mcbond_it	0.559
r_nbtor_refined	0.309

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.846
r_dihedral_angle_4_deg	21.68
r_dihedral_angle_3_deg	15.737
r_dihedral_angle_1_deg	5.49
r_scangle_it	2.101
r_scbond_it	1.468
r_angle_refined_deg	1.338
r_mcangle_it	0.985
r_mcbond_it	0.559
r_nbtor_refined	0.309
r_nbd_refined	0.206
r_symmetry_vdw_refined	0.18
r_xyhbond_nbd_refined	0.126
r_symmetry_hbond_refined	0.112
r_chiral_restr	0.104
r_bond_refined_d	0.015
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2481
Nucleic Acid Atoms
Solvent Atoms	28
Heterogen Atoms	21

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection

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 R01GM133198.