3MDX | pdb_00003mdx

Crystal structure of deoxyuridine 5-triphosphate nucleotidohydrolase from Brucella melitensis, rhombohedral crystal form

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3MBQ	pdb entry 3MBQ, orthorhombic crystal form

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.4	290	MD PACT SCREEN, E12: 20% PEG 3350, 200MM NA MALONATE, BRABA.10050.A AT 9.7MG/ML, pH 7.40, VAPOR DIFFUSION, SITTING DROP, temperature 290K

Crystal Properties
Matthews coefficient	Solvent content
2.24	45.12

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 67.88	α = 90
b = 67.88	β = 90
c = 95.89	γ = 120

Symmetry
Space Group	H 3

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 315r		2010-02-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL7-1		SSRL	BL7-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	1.45	50.12	99.8	0.029	30.1	4.6	29210	29143		-3	23.78

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.45	1.49	100		0.467	3.2	4.6	2204

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 (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 3MBQ, orthorhombic crystal form	1.45	50	29210	29143	1475	99.8	0.151	0.151	0.15	0.16	0.167	0.17	RANDOM	14.88

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]
-0.05	-0.02		-0.05		0.07

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.934
r_dihedral_angle_4_deg	14.104
r_dihedral_angle_3_deg	10.053
r_dihedral_angle_1_deg	7.378
r_scangle_it	4.233
r_scbond_it	2.664
r_mcangle_it	1.856
r_angle_refined_deg	1.683
r_mcbond_it	1.091
r_angle_other_deg	0.978
r_mcbond_other	0.325
r_chiral_restr	0.106
r_bond_refined_d	0.017
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1036
Nucleic Acid Atoms
Solvent Atoms	181
Heterogen Atoms	4

Software

Software
Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling