2V84

Crystal Structure of the Tp0655 (TpPotD) Lipoprotein of Treponema pallidum

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	293	CRYSTALS WERE GROWN AT 20 DEGRRES C USING THE VAPOR DIFFUSION METHOD IN HANGING DROP MODE BY MIXING 1 MICROLITER PROTEIN (20 MG/ML) IN 20 MM HEPES, PH 7.0, 0.1 M NACL, 2 MM BETA-OCTYL GLUCOSIDE WITH 1 MICROLITER RESERVOIR SOLUTION (10-12% (W/V) PEG 20K, 0.1 M MES, PH 6.5) AND EQUILIBRATING AGAINST 1 ML OF RESERVOIR SOLUTION. CRYSTALS APPEARED WITHIN SEVERAL HOURS AND GREW TO A FINAL SIZE OF 0.2 X 0.2 X 0.8 MM IN ABOUT 2 DAYS. THE CRYSTALS WERE CRYO-PROTECTED IN RESERVOIR SOLUTION SUPPLEMENTED WITH 20% (V/V) ETHYLENE GLYCOL, AND THEN FLASH-COOLED IN LIQUID NITROGEN.

Crystal Properties
Matthews coefficient	Solvent content
2.5	52

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 51.61	α = 90
b = 86.27	β = 90
c = 89.5	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	100	CCD	CUSTOM		2007-02-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-BM		APS	19-BM

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	1.78	31.04	99.7	0.05	39.4	6.7		39206		-3	29.6

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)
1	1.78	1.8	97.2		0.83	2	4.4

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	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	SAD	THROUGHOUT	NONE	1.78	30	35504	1893	95.3	0.236	0.234	0.26	RANDOM	32.7

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]
0.17			-0.53		0.36

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.754
r_dihedral_angle_3_deg	15.491
r_dihedral_angle_4_deg	14.178
r_dihedral_angle_1_deg	5.638
r_scangle_it	2.415
r_scbond_it	1.658
r_angle_refined_deg	1.289
r_mcangle_it	1.075
r_mcbond_it	0.645
r_nbtor_refined	0.312
r_symmetry_vdw_refined	0.256
r_nbd_refined	0.201
r_symmetry_hbond_refined	0.184
r_xyhbond_nbd_refined	0.152
r_chiral_restr	0.102
r_bond_refined_d	0.011
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_refined
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_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2575
Nucleic Acid Atoms
Solvent Atoms	128
Heterogen Atoms	29

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
HKL-3000	phasing