2PAR | pdb_00002par

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

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, 0.8 % w/v NDSB 256, 5 % w/v PEG 3350, 1 % v/v Glycerol, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.18	43.58

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 136.136	α = 90
b = 136.136	β = 90
c = 55.418	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)	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	50	100	0.081	8	5.1	22238	22238		-3	41.5

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	2.1	2.14	84		0.423	2.8	5.1

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	40.39	21608	21608	1102		0.196	0.196	0.194	0.2	0.247	0.25	RANDOM	26.96

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]
-0.28	-0.14		-0.28		0.42

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.212
r_dihedral_angle_4_deg	17.153
r_dihedral_angle_3_deg	15.286
r_dihedral_angle_1_deg	6.623
r_scangle_it	3.518
r_scbond_it	2.406
r_angle_refined_deg	1.842
r_mcangle_it	1.36
r_angle_other_deg	0.932
r_mcbond_it	0.926
r_symmetry_vdw_other	0.32
r_mcbond_other	0.276
r_nbd_refined	0.232
r_symmetry_vdw_refined	0.206
r_nbtor_refined	0.189
r_nbd_other	0.181
r_xyhbond_nbd_refined	0.169
r_chiral_restr	0.102
r_nbtor_other	0.092
r_symmetry_hbond_refined	0.081
r_bond_refined_d	0.02
r_bond_other_d	0.009
r_gen_planes_refined	0.008
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	2741
Nucleic Acid Atoms
Solvent Atoms	42
Heterogen Atoms	51

Software

Software
Software Name	Purpose
HKL-2000	data collection
HKL-2000	data reduction
REFMAC	refinement
HKL-3000	data collection
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing
MOLREP	phasing