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Crystal Structure of BthTX-II (Asp49-PLA2 from Bothrops jararacussu snake venom) with calcium ions
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2OQD pdb entry 2OQD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 291 2-propanol, PEG 4000, sodium citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.03 39.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.236 α = 90 b = 100.879 β = 126 c = 47.166 γ = 90
Symmetry Space Group C 1 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 MARMOSAIC 225 mm CCD Mirrors 2009-05-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON LNLS BEAMLINE W01B-MX2 1.425 LNLS W01B-MX2
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 2.1 40 97.4 0.104 10.79 3.7 13058 -3
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 2.1 2.2 99.4 0.51 2.55 3.5
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 pdb entry 2OQD 2.1 50.44 12101 614 97.19 0.21877 0.21719 0.2156 0.24874 0.2463 RANDOM 39.724
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 2.78 -1.11 3.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.31 r_dihedral_angle_3_deg 21.086 r_dihedral_angle_4_deg 20.928 r_dihedral_angle_1_deg 6.591 r_scangle_it 4.137 r_scbond_it 3.07 r_mcangle_it 1.953 r_rigid_bond_restr 1.725 r_angle_refined_deg 1.673 r_mcbond_it 1.299
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.31 r_dihedral_angle_3_deg 21.086 r_dihedral_angle_4_deg 20.928 r_dihedral_angle_1_deg 6.591 r_scangle_it 4.137 r_scbond_it 3.07 r_mcangle_it 1.953 r_rigid_bond_restr 1.725 r_angle_refined_deg 1.673 r_mcbond_it 1.299 r_nbtor_refined 0.316 r_symmetry_hbond_refined 0.282 r_nbd_refined 0.247 r_symmetry_vdw_refined 0.235 r_xyhbond_nbd_refined 0.186 r_chiral_restr 0.111 r_bond_refined_d 0.019 r_gen_planes_refined 0.009 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_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1892 Nucleic Acid Atoms Solvent Atoms 88 Heterogen Atoms 4
Software Software Software Name Purpose MAR345dtb data collection AMoRE phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling