3HZD

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


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
otherModel 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
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.529826% PEG 4000, 0.1M Tris-HCl pH 8.5, 0.2M Lithium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.0840.84

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 55.671α = 90
b = 55.671β = 90
c = 127.836γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mm2007-06-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONLNLS BEAMLINE D03B-MX11.425LNLSD03B-MX1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.9126.649217151162081

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTModel not deposited in the PDB but described in paper by M.T. da Silva-Giotto et al., Proteins (1998), 30, pp. 442 454.1.9126.641620885892.410.217250.215340.25209RANDOM41.503
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]
-0.07-0.03-0.070.1
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.02
r_dihedral_angle_4_deg22.279
r_dihedral_angle_3_deg17.909
r_rigid_bond_restr11.167
r_scbond_it10.125
r_sphericity_free9.516
r_scangle_it8.225
r_dihedral_angle_1_deg6.398
r_sphericity_bonded5.541
r_mcangle_it3.244
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.02
r_dihedral_angle_4_deg22.279
r_dihedral_angle_3_deg17.909
r_rigid_bond_restr11.167
r_scbond_it10.125
r_sphericity_free9.516
r_scangle_it8.225
r_dihedral_angle_1_deg6.398
r_sphericity_bonded5.541
r_mcangle_it3.244
r_mcbond_it2.452
r_angle_refined_deg1.889
r_symmetry_hbond_refined0.351
r_nbtor_refined0.326
r_symmetry_vdw_refined0.313
r_nbd_refined0.24
r_xyhbond_nbd_refined0.197
r_chiral_restr0.113
r_bond_refined_d0.02
r_gen_planes_refined0.008
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 AtomsNumber
Protein Atoms1906
Nucleic Acid Atoms
Solvent Atoms174
Heterogen Atoms1

Software

Software
Software NamePurpose
HKL-2000data collection
AMoREphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling