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Crystal structure of PLA2 from snake venom of peruvian Bothrops atrox
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1MC2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293.15 20% (v/v) 2-propanol, 20% (w/v) polyethylene Glycol 4000 and 0.1 M Sodium Citrate
Crystal Properties Matthews coefficient Solvent content 2.19 43.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36.4 α = 90 b = 58.36 β = 90 c = 64.46 γ = 90
Symmetry Space Group P 2 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 PIXEL DECTRIS PILATUS 2M 2016-05-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON LNLS BEAMLINE W01B-MX2 1.45863 LNLS W01B-MX2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) 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 1.95 43.263 99.7 0.099 0.126 0.062 5.8 4 10474 10474
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.95 2.06 99.9 0.322 0.322 0.403 0.193 1.5 4.1
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 (All) 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 1MC2 1.95 43.263 10451 1099 99.505 0.192 0.1869 0.1866 0.2331 0.2343 RANDOM 27.034
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] 0.431 -0.32 -0.111
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.857 r_dihedral_angle_4_deg 22.762 r_dihedral_angle_3_deg 16.161 r_dihedral_angle_1_deg 6.296 r_lrange_it 6.118 r_scangle_it 3.147 r_mcangle_it 2.71 r_scbond_it 1.948 r_angle_refined_deg 1.846 r_mcbond_it 1.6
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.857 r_dihedral_angle_4_deg 22.762 r_dihedral_angle_3_deg 16.161 r_dihedral_angle_1_deg 6.296 r_lrange_it 6.118 r_scangle_it 3.147 r_mcangle_it 2.71 r_scbond_it 1.948 r_angle_refined_deg 1.846 r_mcbond_it 1.6 r_nbtor_refined 0.311 r_nbd_refined 0.218 r_symmetry_nbd_refined 0.183 r_xyhbond_nbd_refined 0.169 r_symmetry_xyhbond_nbd_refined 0.161 r_chiral_restr 0.12 r_bond_refined_d 0.01 r_gen_planes_refined 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 958 Nucleic Acid Atoms Solvent Atoms 100 Heterogen Atoms 14
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling SIMBAD phasing