2PAU | pdb_00002pau

Crystal structure of the 5'-deoxynucleotidase YfbR mutant E72A complexed with Co(2+) and dAMP

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1WPH	PDB entry 1WPH

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5	293	0.1 M NH4 Citrate, 0.1 % w/v NDSB 256, 5 % w/v PEG 3350, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.14	42.52

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 135.595	α = 90
b = 135.595	β = 90
c = 54.936	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 315	LN2 cooled first crystal, sagital focusing 2nd crystal, Rosenbaum-Rock vertical focusing mirror, beam defining slits	2006-06-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.97937	APS	19-ID

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	50	100	0.066	0.066	9.6	4.4	25437	25437		-3	45.7

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	2.07	82.7		0.563	0.563	2	4.4

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 1WPH	2.1	40.13	19971	19971	1028		0.196	0.196	0.193	0.21	0.26	0.24	RANDOM	41.53

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]
-0.13	-0.06		-0.13		0.19

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.108
r_dihedral_angle_4_deg	17.821
r_dihedral_angle_3_deg	15.351
r_dihedral_angle_1_deg	6.341
r_scangle_it	3.615
r_scbond_it	2.411
r_angle_refined_deg	1.908
r_mcangle_it	1.45
r_mcbond_it	0.983
r_angle_other_deg	0.902
r_symmetry_vdw_refined	0.337
r_symmetry_vdw_other	0.33
r_mcbond_other	0.276
r_nbd_refined	0.238
r_nbtor_refined	0.19
r_nbd_other	0.183
r_xyhbond_nbd_refined	0.168
r_symmetry_hbond_refined	0.145
r_chiral_restr	0.104
r_nbtor_other	0.093
r_bond_refined_d	0.022
r_gen_planes_refined	0.007
r_bond_other_d	0.002
r_gen_planes_other	0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
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	2724
Nucleic Acid Atoms
Solvent Atoms	53
Heterogen Atoms	53

Software

Software
Software Name	Purpose
HKL-3000	data collection
HKL-3000	data reduction
REFMAC	refinement
HKL-3000	data scaling
HKL-3000	phasing
MOLREP	phasing