3B9X

Crystal structure of the E. coli pyrimidine nucleoside hydrolase YeiK in complex with inosine

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1Q8F	PDB ENTRY 1Q8F

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	293	0.1M Tris-HCl, 0.2M NaCl, 24% PEG 4000, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.12	41.99

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 45.112	α = 67.9
b = 82.406	β = 79.59
c = 90.163	γ = 89.65

Symmetry
Space Group	P 1

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++	Osmic	2007-05-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007	1.5418

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	2.3	100	95.4	0.102	0.095	18.7	7.3	50148	50148		-3	28.3

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	2.3	2.45	92.6		0.255	0.235	8.9	6.7	5843

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1Q8F	2.3	81.92	48587	48587	1560	95.58	0.203	0.201	0.255	RANDOM	22.98

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]
1.19	0.54	0.51	-0.23	0.02	-1.16

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.082
r_dihedral_angle_4_deg	17.026
r_dihedral_angle_3_deg	15.107
r_dihedral_angle_1_deg	6.368
r_scangle_it	4.728
r_scbond_it	3.759
r_mcangle_it	3.389
r_mcbond_it	2.516
r_angle_refined_deg	1.473
r_symmetry_vdw_refined	0.303
r_nbtor_refined	0.301
r_symmetry_hbond_refined	0.259
r_nbd_refined	0.205
r_xyhbond_nbd_refined	0.163
r_metal_ion_refined	0.13
r_chiral_restr	0.092
r_bond_refined_d	0.016
r_gen_planes_refined	0.005
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_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	9030
Nucleic Acid Atoms
Solvent Atoms	331
Heterogen Atoms	91

Software

Software
Software Name	Purpose
REFMAC	refinement
CrystalClear	data collection
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing