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Crystal Structure of Myotoxin II (MjTX-II), a myotoxic Lys49-phospholipase A2 from Bothrops moojeni.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1XXS PDB ENTRY 1XXS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 291 20% (v/v) 2-propanol, 20% (w/v) polyethylene Glycol 4000 and 0.1 M Sodium Citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.4 48.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.999 α = 90 b = 62.169 β = 90 c = 86.007 γ = 90
Symmetry Space Group P 21 21 21
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 2012-03-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON LNLS BEAMLINE W01B-MX2 1.42 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 1.92 50 92.4 0.044 10.37 3.9 19571 -3 24.6
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 1.92 1.99 97.6 0.41 2.01 3.7
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 1XXS 1.92 38.96 19491 19491 945 92.4 0.227 0.227 0.227 0.2315 0.257 0.2603 Random 56.13
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] -4.9 -5.45 10.35
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 21.9 c_angle_deg 2.1 c_improper_angle_d 0.76 c_angle_d 0.03
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1873 Nucleic Acid Atoms Solvent Atoms 185 Heterogen Atoms 120
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing CNS refinement DENZO data reduction SCALEPACK data scaling