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Crystal structure of bothropstoxin-I (BthTX-I), a PLA2 homologue from Bothrops jararacussu venom
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 (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) 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 0.2235 0.25209 0.2563 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
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