2J4L

Crystal structure of uridylate kinase from Sulfolobus solfataricus in complex with UTP to 2.8 Angstrom resolution

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
other		URIDYLATE KINASE FROM SULFOLOBUS SOLFATARICUS IN COMPLEX WITH UMP AND AMPPCP - HEXAMER - WITHOUT LIGANDS

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.8		PROTEIN SOLUTION (2UL) IN 10 MM TRIS/CL PH 7.6 WITH 4.6 MG/ML SSUMPK, 2 MM UTP, 5 MM MGCL2 MIXED WITH 2UL MOTHER SOLUTION. MOTHER SOLUTION: 1.8 M SODIUM FORMATE, 0.1 M SODIUM ACETATE PH 4.8. HANGIGN DROP VAPOR DIFFUSION

Crystal Properties
Matthews coefficient	Solvent content
3.32	60.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 224.75	α = 90
b = 79.03	β = 96.56
c = 223.47	γ = 90

Symmetry
Space Group	C 1 2 1

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	MARRESEARCH	MULTILAYER MIRRORS	2005-06-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	MAX II BEAMLINE I911-3		MAX II	I911-3

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	2.8	40.52	94.5	0.08	12.7	4.3		92163		-3	56.5

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	2.8	2.95	85.9		0.54	1.9	4.2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	URIDYLATE KINASE FROM SULFOLOBUS SOLFATARICUS IN COMPLEX WITH UMP AND AMPPCP - HEXAMER - WITHOUT LIGANDS	2.8	29.63	91357	4593	94.6	0.246	0.246	0.278	RANDOM	76.9

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]
-11.74		0.6	28.4		-16.66

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	22.1
c_scangle_it	2.88
c_mcangle_it	2.39
c_scbond_it	1.75
c_angle_deg	1.5
c_mcbond_it	1.35
c_improper_angle_d	0.9
c_bond_d	0.009
c_bond_d_na
c_bond_d_prot
c_angle_d
c_angle_d_na
c_angle_d_prot
c_angle_deg_na
c_angle_deg_prot
c_dihedral_angle_d_na
c_dihedral_angle_d_prot
c_improper_angle_d_na
c_improper_angle_d_prot

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	19258
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	355

Software

Software
Software Name	Purpose
CNS	refinement
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing