3HZD

Crystal structure of bothropstoxin-I (BthTX-I), a PLA2 homologue from Bothrops jararacussu venom

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
other		Model not deposited in the PDB but described in paper by M.T. da Silva-Giotto et al., Proteins (1998), 30, pp. 442 454.

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	298	26% PEG 4000, 0.1M Tris-HCl pH 8.5, 0.2M Lithium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.08	40.84

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 55.671	α = 90
b = 55.671	β = 90
c = 127.836	γ = 120

Symmetry
Space Group	P 31 2 1

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	MAR CCD 165 mm		2007-06-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	LNLS BEAMLINE D03B-MX1	1.425	LNLS	D03B-MX1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.91	26.64	92			17151	16208		1

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	MOLECULAR REPLACEMENT	THROUGHOUT	Model not deposited in the PDB but described in paper by M.T. da Silva-Giotto et al., Proteins (1998), 30, pp. 442 454.	1.91	26.64	16208	858	92.41	0.21725	0.21534	0.25209	RANDOM	41.503

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]
-0.07	-0.03		-0.07		0.1

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.02
r_dihedral_angle_4_deg	22.279
r_dihedral_angle_3_deg	17.909
r_rigid_bond_restr	11.167
r_scbond_it	10.125
r_sphericity_free	9.516
r_scangle_it	8.225
r_dihedral_angle_1_deg	6.398
r_sphericity_bonded	5.541
r_mcangle_it	3.244
r_mcbond_it	2.452
r_angle_refined_deg	1.889
r_symmetry_hbond_refined	0.351
r_nbtor_refined	0.326
r_symmetry_vdw_refined	0.313
r_nbd_refined	0.24
r_xyhbond_nbd_refined	0.197
r_chiral_restr	0.113
r_bond_refined_d	0.02
r_gen_planes_refined	0.008
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

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1906
Nucleic Acid Atoms
Solvent Atoms	174
Heterogen Atoms	1

Software

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