2O6F | pdb_00002o6f

Structure of metal- free rTp34 from Treponema pallidum

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		native protein

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	9	293	2.4 M Ammonium sulfate, 0.1 M Bicine, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.09	41.06

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 34.251	α = 90
b = 66.034	β = 90
c = 151.019	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-MADE		2006-07-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-BM	0.97899	APS	19-BM

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	1.63	26.03	95.3	0.038	32	4.1	41967	41967		-3	25

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	1.63	1.66	94.1		0.487	2.2	3.7	2016

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	THROUGHOUT	native protein	1.63	26.03	41892	1508	95.11	0.19	0.189	0.1856	0.219	0.215	RANDOM	25.686

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			-1.05		0.05

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.881
r_dihedral_angle_4_deg	17.948
r_dihedral_angle_3_deg	13.975
r_dihedral_angle_1_deg	4.874
r_scangle_it	4.121
r_scbond_it	2.565
r_angle_refined_deg	1.893
r_mcangle_it	1.698
r_mcbond_it	1.081
r_nbtor_refined	0.318
r_symmetry_hbond_refined	0.206
r_nbd_refined	0.198
r_symmetry_vdw_refined	0.184
r_xyhbond_nbd_refined	0.146
r_chiral_restr	0.137
r_bond_refined_d	0.015
r_gen_planes_refined	0.015

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2474
Nucleic Acid Atoms
Solvent Atoms	240
Heterogen Atoms	21

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-3000	data collection
HKL-3000	data reduction
HKL-3000	data scaling
CNS	phasing