3RG8

Crystal structure of Treponema denticola PurE

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1O4V	PDB ENTRY 1o4v

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, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.03	39.51

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 83.47	α = 90
b = 87.92	β = 118.3
c = 86.7	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	110	CCD	NOIR-1	ROSENBAUM-ROCK MONOCHROMATOR 1:HIGH-RESOLUTION DOUBLE-CRYSTAL SAGITTAL FOCUSING, ROSENBAUM-ROCK MONOCHROMATOR 2:DOUBLE CRYSTAL, ROSENBAUM-ROCK VERTICAL FOCUSING MIRROR	2006-09-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 4.2.2	1.24	ALS	4.2.2

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	1.74	19.7	99.5	0.051	17.5	3.6	112698	112698

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	1.74	1.79	99.5		0.591	2.1	3.5	8305

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 1o4v	1.74	19.63	106915	106915	5659	97.22	0.16678	0.16503	0.19974	RANDOM	17.646

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]
-5.04		1.71	-0.56		5.6

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.381
r_dihedral_angle_3_deg	14.264
r_dihedral_angle_4_deg	12.408
r_dihedral_angle_1_deg	5.748
r_scangle_it	3.269
r_scbond_it	2.158
r_angle_refined_deg	1.547
r_mcangle_it	1.232
r_angle_other_deg	1.12
r_mcbond_it	0.796
r_mcbond_other	0.269
r_chiral_restr	0.091
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	9455
Nucleic Acid Atoms
Solvent Atoms	802
Heterogen Atoms	8

Software

Software
Software Name	Purpose
AMoRE	phasing
REFMAC	refinement
d*TREK	data reduction
d*TREK	data scaling