1SYL

Crystal structure of inactive mutant dUTPase complexed with substrate dUTP

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1EUW	PDB ENTRY 1EUW

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.8	293	PEG 3350, SODIUM ACETATE, TRIS, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.6	52.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 76.421	α = 90
b = 76.421	β = 90
c = 100.259	γ = 120

Symmetry
Space Group	P 63 2 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	IMAGE PLATE	MARRESEARCH	mirror	2004-03-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE BW7B	0.8414	EMBL/DESY, HAMBURG	BW7B

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	1.9	20	98.3	0.063	14.97	2.88	13413	13413		-3	32.959

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.91	2.03	98.5		0.484	2.54	2.91	2085

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	PDB ENTRY 1EUW	1.95	20	12350	12350	645	98.62	0.15971	0.15971	0.15821	0.1886	RANDOM	29.501

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]
-0.8	-0.4		-0.8		1.21

RMS Deviations
Key	Refinement Restraint Deviation
r_scangle_it	13.55
r_scbond_it	10.344
r_dihedral_angle_1_deg	6.457
r_mcangle_it	3.137
r_angle_refined_deg	1.686
r_mcbond_it	1.466
r_angle_other_deg	0.838
r_symmetry_hbond_refined	0.366
r_symmetry_vdw_other	0.275
r_nbd_other	0.257
r_xyhbond_nbd_refined	0.24
r_nbd_refined	0.198
r_symmetry_vdw_refined	0.16
r_chiral_restr	0.104
r_nbtor_other	0.087
r_bond_refined_d	0.021
r_gen_planes_refined	0.007
r_gen_planes_other	0.004
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1035
Nucleic Acid Atoms
Solvent Atoms	167
Heterogen Atoms	37

Software

Software
Software Name	Purpose
REFMAC	refinement
MAR345	data collection
XDS	data scaling
MOLREP	phasing