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Crystal structure of Bn IV in complex with myristic acid: A Lys49 myotoxic phospholipase A2 from Bothrops neuwiedi venom
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1PC9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 293 Buffer Tris 0.1 M pH 8.5, PEG 4000 30%, lithium sulphate 0.2M, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.07 40.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.801 α = 90 b = 70.466 β = 109.32 c = 44.006 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 130 mm Mirrors 2008-04-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON LNLS BEAMLINE D03B-MX1 1.423 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 2.203 41.528 96 0.09 0.09 6.5 11.4 11129 10927 2 2
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 2.2 2.32 88.6 0.306 0.32 2.3 3.3
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 (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 1PC9 2.21 32.49 11129 10401 522 96.41 0.20743 0.20506 0.201 0.25328 0.2415 RANDOM 23.853
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] -0.48 -0.09 1.05 -0.57
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.247 r_dihedral_angle_4_deg 25.714 r_dihedral_angle_3_deg 20.84 r_sphericity_free 11.506 r_dihedral_angle_1_deg 8.516 r_scangle_it 6.588 r_sphericity_bonded 5.041 r_scbond_it 5 r_rigid_bond_restr 3.458 r_mcangle_it 3.367
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.247 r_dihedral_angle_4_deg 25.714 r_dihedral_angle_3_deg 20.84 r_sphericity_free 11.506 r_dihedral_angle_1_deg 8.516 r_scangle_it 6.588 r_sphericity_bonded 5.041 r_scbond_it 5 r_rigid_bond_restr 3.458 r_mcangle_it 3.367 r_angle_refined_deg 2.579 r_mcbond_it 2.375 r_chiral_restr 0.146 r_bond_refined_d 0.032 r_gen_planes_refined 0.017 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1896 Nucleic Acid Atoms Solvent Atoms 86 Heterogen Atoms 52
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement MOSFLM data reduction SCALA data scaling