3EHW | pdb_00003ehw

Human dUTPase in complex with alpha,beta-imido-dUTP and Mg2+: visualization of the full-length C-termini in all monomers and suggestion for an additional metal ion binding site

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1Q5U	PDB ENTRY 1Q5U

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	293	0.1 M HEPES buffer, containing 20% PEG 3350 and 200 mM sodium chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
1.89	34.87

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 65.446	α = 90
b = 87.16	β = 90.09
c = 70.608	γ = 90

Symmetry
Space Group	P 1 21 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	MAR CCD 165 mm	BENT, VERTICALLY FOCUSING MIRROR	2004-11-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE X13	0.8031	EMBL/DESY, HAMBURG	X13

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	1.8	20	95.8	0.071	10.15	2.17	70417	70417		-3	26.26

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	1.8	1.9	97.4		0.475	2.24	2.13	10689

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1Q5U	1.8	20	66842	66842	3574	95.84	0.15972	0.1576	0.16	0.19898	0.2	RANDOM	23.11

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]
-0.84		-0.07	0.24		0.6

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.116
r_dihedral_angle_4_deg	17.146
r_dihedral_angle_3_deg	13.382
r_dihedral_angle_1_deg	6.439
r_scangle_it	5.14
r_scbond_it	3.446
r_mcangle_it	1.52
r_angle_refined_deg	1.289
r_mcbond_it	0.875
r_nbtor_refined	0.314
r_nbd_refined	0.195
r_symmetry_vdw_refined	0.191
r_symmetry_hbond_refined	0.174
r_xyhbond_nbd_refined	0.156
r_chiral_restr	0.079
r_metal_ion_refined	0.016
r_bond_refined_d	0.01
r_gen_planes_refined	0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6346
Nucleic Acid Atoms
Solvent Atoms	731
Heterogen Atoms	176

Software

Software
Software Name	Purpose
MOLREP	phasing
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling