1XE3

Crystal Structure of purine nucleoside phosphorylase DeoD from Bacillus anthracis

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	291	PEG 400, magnesium chloride, HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291.0K

Crystal Properties
Matthews coefficient	Solvent content
3	58.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 63.861	α = 90
b = 128.257	β = 90
c = 223.565	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	120	IMAGE PLATE	MARRESEARCH	osmic multilayer mirrors	2004-04-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU	1.54189

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	2.24	20	90.9	0.141		3.9	81257	81257

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)
	2.24	2.32	82		0.502	1.84	3.2	7218

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1ECP	2.24	20	81055	81055	4065	100	0.18369	0.18369	0.18097	0.23523	RANDOM	20.373

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]
0.56			0.18		-0.74

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.894
r_dihedral_angle_3_deg	18.661
r_dihedral_angle_4_deg	14.394
r_dihedral_angle_1_deg	6.807
r_scangle_it	2.567
r_scbond_it	1.685
r_angle_refined_deg	1.538
r_angle_other_deg	0.963
r_mcangle_it	0.907
r_mcbond_it	0.75
r_symmetry_vdw_other	0.317
r_symmetry_vdw_refined	0.217
r_nbd_refined	0.192
r_nbd_other	0.191
r_nbtor_refined	0.174
r_symmetry_hbond_refined	0.17
r_xyhbond_nbd_refined	0.166
r_mcbond_other	0.113
r_chiral_restr	0.108
r_nbtor_other	0.089
r_bond_refined_d	0.014
r_gen_planes_refined	0.004
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10728
Nucleic Acid Atoms
Solvent Atoms	716
Heterogen Atoms	6

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing