2OKB | pdb_00002okb

High Resolution Crystal Structures of Vaccinia Virus dUTPase

X-RAY DIFFRACTION

---

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		4.2	298	12% PEG1000, 0.1M lithium sulfate, 0.1M phosphate/citrate buffer, pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K, pH 4.20

Crystal Properties
Matthews coefficient	Solvent content
2.09	41.05

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 105.26	α = 90
b = 105.26	β = 90
c = 59.29	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	IMAGE PLATE	RIGAKU RAXIS IV	MIRRORS	2005-06-05	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	2.15	49.7	98.6	0.033	0.033	29.9	6.2		20238		1	27

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	2.15	2.23	92.1		0.144	0.144	6	2.6

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	2.15	18.13	19126	19126	1034	98.4	0.212	0.21	0.23	0.257	0.27	RANDOM	30.84

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]
0.03	0.01		0.03		-0.04

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	27.801
r_dihedral_angle_4_deg	13.583
r_dihedral_angle_3_deg	11.892
r_dihedral_angle_1_deg	5.671
r_scangle_it	1.101
r_angle_refined_deg	0.902
r_scbond_it	0.697
r_mcangle_it	0.548
r_mcbond_it	0.31
r_nbtor_refined	0.309
r_nbd_refined	0.161
r_symmetry_vdw_refined	0.146
r_symmetry_hbond_refined	0.116
r_xyhbond_nbd_refined	0.101
r_chiral_restr	0.058
r_bond_refined_d	0.007
r_gen_planes_refined	0.002
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	2643
Nucleic Acid Atoms
Solvent Atoms	236
Heterogen Atoms	29

Software

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