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Crystal structure of the myotoxin-II from Atropoides nummifer venom
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1MC2 PDB entry: 1MC2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 293 ammonium sulfate, peg 3350, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.66 53.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.939 α = 90 b = 68.939 β = 90 c = 64.069 γ = 90
Symmetry Space Group P 43 21 2
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 MARRESEARCH 2004-05-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON LNLS BEAMLINE D03B-MX1 1.427 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 2.08 30.36 99.1 9671 9272 1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.08 2.19 94.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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: 1MC2 2.08 30.36 9671 9203 466 99.41 0.2315 0.22148 0.21895 0.2264 0.27502 0.2295 RANDOM 30.485
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] -1.02 -1.02 2.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.96 r_scangle_it 2.471 r_scbond_it 1.65 r_angle_refined_deg 1.398 r_mcangle_it 0.907 r_mcbond_it 0.498 r_symmetry_hbond_refined 0.32 r_symmetry_vdw_refined 0.298 r_xyhbond_nbd_refined 0.249 r_nbd_refined 0.228
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.96 r_scangle_it 2.471 r_scbond_it 1.65 r_angle_refined_deg 1.398 r_mcangle_it 0.907 r_mcbond_it 0.498 r_symmetry_hbond_refined 0.32 r_symmetry_vdw_refined 0.298 r_xyhbond_nbd_refined 0.249 r_nbd_refined 0.228 r_chiral_restr 0.093 r_bond_refined_d 0.014 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 946 Nucleic Acid Atoms Solvent Atoms 71 Heterogen Atoms 5
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing