1RNJ

Crystal structure of inactive mutant dUTPase complexed with substrate analogue imido-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
2.55	51.3

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 74.9	α = 90
b = 74.9	β = 90
c = 99.643	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	ADSC QUANTUM 4		2003-03-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-4	0.9392	ESRF	ID14-4

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	1.7	22	98.2	0.059	8.4	20.32		18342

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	1.7	1.74	98.2		0.38	2	20.81	1268

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	1.7	20	17392	17392	949	98.2	0.18	0.15812	0.15654	0.1872	RANDOM	19.221

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]
-0.31	-0.15		-0.31		0.46

RMS Deviations
Key	Refinement Restraint Deviation
r_scangle_it	9.45
r_scbond_it	7.396
r_dihedral_angle_1_deg	5.865
r_mcangle_it	4.712
r_angle_other_deg	2.576
r_mcbond_it	2.354
r_angle_refined_deg	1.537
r_symmetry_vdw_other	0.322
r_nbd_other	0.278
r_xyhbond_nbd_refined	0.219
r_symmetry_hbond_refined	0.194
r_nbd_refined	0.182
r_symmetry_vdw_refined	0.15
r_metal_ion_refined	0.146
r_nbtor_other	0.094
r_chiral_restr	0.088
r_bond_refined_d	0.019
r_gen_planes_refined	0.005
r_gen_planes_other	0.005
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1069
Nucleic Acid Atoms
Solvent Atoms	221
Heterogen Atoms	37

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
CCP4	data scaling
MOLREP	phasing