2PAQ | pdb_00002paq

Crystal structure of the 5'-deoxynucleotidase YfbR

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5	293	10% w/v PEG 3350, 0.3 M NH4 CITRATE, 5 mM BETA-MERCAPTOETHANOL, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.24	45.09

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 137.023	α = 90
b = 137.023	β = 90
c = 56.288	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	SBC-3	LN2 cooled first crystal, sagital focusing 2nd crystal, Rosenbaum-Rock vertical focusing mirror, beam-defining slits	2004-02-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.97929	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	1.95	50	98.2	0.099	0.099	24.9	5	28633	28633		-3	39.7

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	1.95	2.02	87.8		0.58	0.58	1.4	3.6

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	SAD	THROUGHOUT	2.1	28.41	22944	22944	1172		0.19	0.19	0.187	0.19	0.237	0.24	RANDOM	26.58

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]
-1.48	-0.74		-1.48		2.22

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.268
r_dihedral_angle_3_deg	15.664
r_dihedral_angle_4_deg	14.635
r_dihedral_angle_1_deg	6.57
r_scangle_it	4.322
r_scbond_it	3.08
r_angle_refined_deg	1.805
r_mcangle_it	1.624
r_mcbond_it	1.332
r_angle_other_deg	0.926
r_symmetry_vdw_refined	0.45
r_symmetry_vdw_other	0.343
r_mcbond_other	0.308
r_nbd_refined	0.227
r_symmetry_hbond_refined	0.195
r_nbd_other	0.191
r_xyhbond_nbd_refined	0.191
r_nbtor_refined	0.186
r_chiral_restr	0.105
r_nbtor_other	0.093
r_bond_refined_d	0.022
r_gen_planes_refined	0.007
r_bond_other_d	0.001
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	2793
Nucleic Acid Atoms
Solvent Atoms	124
Heterogen Atoms

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
DM	phasing
MLPHARE	phasing
SHELXD	phasing
SHELXE	model building
O	model building
CCP4	phasing
SOLVE	phasing
RESOLVE	phasing
ARP/wARP	model building
SHARP	phasing
autoSHARP	phasing