3K3F | pdb_00003k3f

Crystal Structure of the Urea Transporter from Desulfovibrio Vulgaris

X-RAY DIFFRACTION

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Crystallization

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

Crystal Properties
Matthews coefficient	Solvent content
4.14	70.25

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 110.131	α = 90
b = 110.131	β = 90
c = 84.861	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 315r		2009-05-02		SINGLE WAVELENGTH
2	1	x-ray	100		SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X29A	1.01	NSLS	X29A
2	SYNCHROTRON	NSLS BEAMLINE X29A	1.04	NSLS	X29A

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	2.3	50	99.4	0.089	14.4	8.2	26094	25924

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	2.3	2.34	95.2		0.964		5.2	1214

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	2.3	38.78	25854	25854	1293	99.21	0.18	0.18	0.179	0.1812	0.204	0.2064	RANDOM	48.581

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]
0.7	0.35		0.7		-1.05

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.836
r_dihedral_angle_3_deg	17.03
r_dihedral_angle_4_deg	14.56
r_dihedral_angle_1_deg	6.04
r_scangle_it	3.204
r_scbond_it	2.183
r_angle_refined_deg	1.469
r_mcangle_it	1.283
r_mcbond_it	0.767
r_nbtor_refined	0.31
r_nbd_refined	0.209
r_symmetry_vdw_refined	0.204
r_xyhbond_nbd_refined	0.133
r_symmetry_hbond_refined	0.103
r_chiral_restr	0.1
r_bond_refined_d	0.018
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2485
Nucleic Acid Atoms
Solvent Atoms	55
Heterogen Atoms	9

Software

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