3TS6

Crystal structure of M-PMV DUTPASE relaxed end-product (dUMP) complex

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	293	PEG 8000, AMMONIUM CHLORIDE, TRIS, PH 8.5 , VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.09	41.1

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 60.682	α = 90
b = 60.682	β = 90
c = 63.544	γ = 120

Symmetry
Space Group	P 63

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	MIRRORS	2004-11-26	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	1.84	52.56	98.3	0.041	17.1	2.9	11408	11408		-3

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	1.94	99.5		0.359	3.7	2.8	1679

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	RIGID BODY REFINEMENT	THROUGHOUT	PDB ENTRY 2D4L	1.84	20	10798	610	98.26	0.16885	0.16698	0.20113	RANDOM	29.492

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]
1.34	0.67		1.34		-2.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	42.009
r_dihedral_angle_4_deg	16.925
r_dihedral_angle_3_deg	15.89
r_dihedral_angle_1_deg	11.668
r_scangle_it	7.581
r_scbond_it	5.302
r_mcangle_it	3.208
r_angle_refined_deg	1.994
r_mcbond_it	1.974
r_nbtor_refined	0.328
r_symmetry_hbond_refined	0.234
r_nbd_refined	0.228
r_symmetry_vdw_refined	0.199
r_xyhbond_nbd_refined	0.193
r_chiral_restr	0.121
r_bond_refined_d	0.019
r_gen_planes_refined	0.009
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_refined
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	803
Nucleic Acid Atoms
Solvent Atoms	119
Heterogen Atoms	20

Software

Software
Software Name	Purpose
MAR345	data collection
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
REFMAC	phasing