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Crystal Structure of Bothropstoxin-I complexed with polietilene glicol 4000 - crystallized at 283 K
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3HZD PDB entry (3HZD)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 283 29% PEG 4000, 0.1M Tris HCl, 0.2M Lithium Sulfate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 283.0K
Crystal Properties Matthews coefficient Solvent content 2.12 41.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.5 α = 90 b = 70.8 β = 102.2 c = 43.8 γ = 90
Symmetry Space Group P 1 21 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 Mirrors 2007-10-10 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) R Merge I (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 1.55 50 98.2 0.067 0.067 12.73 3.3 32689 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.55 1.62 99.4 0.439 0.439 1.82 3.2
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 (3HZD) 1.55 18.32 30990 1652 98.25 0.20291 0.20049 0.2105 0.24647 0.2506 RANDOM 30.019
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] 0.01 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.865 r_dihedral_angle_4_deg 19.752 r_dihedral_angle_3_deg 14.602 r_dihedral_angle_1_deg 5.661 r_sphericity_free 5.26 r_scangle_it 4 r_scbond_it 3.864 r_rigid_bond_restr 3.805 r_sphericity_bonded 2.987 r_mcangle_it 1.778
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.865 r_dihedral_angle_4_deg 19.752 r_dihedral_angle_3_deg 14.602 r_dihedral_angle_1_deg 5.661 r_sphericity_free 5.26 r_scangle_it 4 r_scbond_it 3.864 r_rigid_bond_restr 3.805 r_sphericity_bonded 2.987 r_mcangle_it 1.778 r_angle_refined_deg 1.632 r_mcbond_it 1.195 r_nbtor_refined 0.328 r_nbd_refined 0.249 r_symmetry_vdw_refined 0.184 r_xyhbond_nbd_refined 0.149 r_symmetry_hbond_refined 0.145 r_chiral_restr 0.088 r_bond_refined_d 0.014 r_gen_planes_refined 0.007 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 241 Heterogen Atoms 82
Software Software Software Name Purpose HKL-2000 data collection AMoRE phasing REFMAC refinement DENZO data reduction SCALEPACK data scaling