2HR6

Crystal structure of dUTPase in complex with substrate analogue dUDP and manganese

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.8	293	20% PEG 3350, 0.2M SODIUM ACETATE, 0.1M TRIS, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.49	50.61

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 75.049	α = 90
b = 75.049	β = 90
c = 99.936	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	CCD	MAR CCD 165 mm	mirror	2002-03-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE X11	0.8110	EMBL/DESY, HAMBURG	X11

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	1.84	24.9	98	0.064	10.8	12.6	14703	14703		-3	22.35

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	1.84	1.89	98		0.558	1.3	10.1	815

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	1EUW	1.84	24.9	13953	13953	749	98.1	0.15168	0.15168	0.15054	0.17338	RANDOM	22.763

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]
-0.09	-0.04		-0.09		0.13

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.32
r_dihedral_angle_4_deg	16.193
r_dihedral_angle_3_deg	12.121
r_scangle_it	7.993
r_scbond_it	6.01
r_dihedral_angle_1_deg	5.818
r_mcangle_it	3.606
r_mcbond_it	2.23
r_angle_refined_deg	1.702
r_angle_other_deg	0.821
r_symmetry_hbond_refined	0.284
r_symmetry_vdw_other	0.251
r_nbd_refined	0.215
r_xyhbond_nbd_refined	0.203
r_nbd_other	0.191
r_symmetry_vdw_refined	0.171
r_nbtor_refined	0.164
r_chiral_restr	0.098
r_mcbond_other	0.093
r_nbtor_other	0.082
r_bond_refined_d	0.016
r_gen_planes_refined	0.007
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1013
Nucleic Acid Atoms
Solvent Atoms	156
Heterogen Atoms	29

Software

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