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Structure of MTX-II from Bothrops brazili
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2H8I pdb entry 2H8I
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.2 291 0.1 M tris pH 8.2, 25% PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.22 44.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.4 α = 90 b = 128.886 β = 105.66 c = 67.008 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 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON LNLS BEAMLINE W01B-MX2 1.458 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 2.7 20 94.2 0.116 3 13286 12516
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 2.7 2.8 86.1 0.339 2.68 2.7 1132
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 2H8I 2.7 19.72 11881 629 93.93 0.2276 0.22267 0.2363 0.31981 0.3252 RANDOM 36.954
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] 0.1 -0.16 0.04 -0.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.077 r_dihedral_angle_4_deg 21.345 r_dihedral_angle_3_deg 21.176 r_dihedral_angle_1_deg 6.926 r_scangle_it 2.412 r_angle_refined_deg 1.472 r_scbond_it 1.396 r_mcangle_it 1.063 r_mcbond_it 0.531 r_chiral_restr 0.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.077 r_dihedral_angle_4_deg 21.345 r_dihedral_angle_3_deg 21.176 r_dihedral_angle_1_deg 6.926 r_scangle_it 2.412 r_angle_refined_deg 1.472 r_scbond_it 1.396 r_mcangle_it 1.063 r_mcbond_it 0.531 r_chiral_restr 0.1 r_bond_refined_d 0.012 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3837 Nucleic Acid Atoms Solvent Atoms 102 Heterogen Atoms 26
Software Software Software Name Purpose MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling