3RGG

Crystal structure of Treponema denticola PurE bound to AIR

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		Native coordinate

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	298	14-16% (W/V) PEG 1000, 0.1 M MAGNESIUM CHLORIDE, 0.1 M IMIDAZOLE, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.09	41.12

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 84.39	α = 90
b = 155.13	β = 90
c = 88.14	γ = 90

Symmetry
Space Group	C 2 2 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	111	IMAGE PLATE	RIGAKU RAXIS IV		2006-10-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU200	1.54

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.82	37.1	98.6	0.064	20	6.4	51257	51257

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.82	1.87	92.3		0.865	2.2	5.1	3520

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	Native coordinate	1.82	37.1	48510	48510	2607	98.34	0.18985	0.18816	0.22155	RANDOM	28.749

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]
-0.84			2.22		-1.38

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.951
r_dihedral_angle_3_deg	14.381
r_dihedral_angle_4_deg	12.906
r_dihedral_angle_1_deg	5.792
r_scangle_it	3.362
r_scbond_it	2.183
r_angle_refined_deg	1.674
r_mcangle_it	1.212
r_angle_other_deg	0.98
r_mcbond_it	0.731
r_mcbond_other	0.216
r_chiral_restr	0.089
r_bond_refined_d	0.016
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
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	4703
Nucleic Acid Atoms
Solvent Atoms	283
Heterogen Atoms	76

Software

Software
Software Name	Purpose
HKL-2000	data collection
AMoRE	phasing
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling