2OL0 | pdb_00002ol0

High Resolution Crystal Structures of Vaccinia Virus dUTPase

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2OKD	PDB ENTRY 2OKD

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7	298	20% PEG2000 MME, 0.1M Tris, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K, pH 7.00

Crystal Properties
Matthews coefficient	Solvent content
2.12	41.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 119.66	α = 90
b = 119.66	β = 90
c = 50.16	γ = 120

Symmetry
Space Group	P 65

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	RIGAKU RAXIS IV	MIRRORS	2006-06-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU200

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.1	19.94	99.5	0.078	0.078	10.2	3.6		24014		1	23

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.1	2.18	99		0.347	0.347	3.4	3.5

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 2OKD	2.1	19.58	22718	22718	1156	99.6	0.209	0.207	0.22	0.261	0.27	RANDOM	24.55

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.469
r_dihedral_angle_4_deg	21.186
r_dihedral_angle_3_deg	14.437
r_dihedral_angle_1_deg	5.967
r_scangle_it	1.698
r_angle_refined_deg	1.188
r_scbond_it	1.022
r_mcangle_it	0.599
r_mcbond_it	0.348
r_nbtor_refined	0.31
r_nbd_refined	0.19
r_symmetry_hbond_refined	0.181
r_symmetry_vdw_refined	0.151
r_xyhbond_nbd_refined	0.138
r_chiral_restr	0.066
r_bond_refined_d	0.008
r_gen_planes_refined	0.003
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	2915
Nucleic Acid Atoms
Solvent Atoms	206
Heterogen Atoms	86

Software

Software
Software Name	Purpose
REFMAC	refinement
d*TREK	data reduction
d*TREK	data scaling
MOLREP	phasing