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Crystal structure of russells viper phospholipase A2 in complex with a specifically designed tetrapeptide Ala-Ile-Arg-Ser at 1.1 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1SKG PDB entry 1SKG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 298 0.2M AMMONIUM SULPHATE, 30% PEG , pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.5 50
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.512 α = 90 b = 52.512 β = 90 c = 48.088 γ = 90
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 200 CCD MARRESEARCH mirror 2004-04-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X11 0.806 EMBL/DESY, HAMBURG X11
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.1 50 100 0.041 22.9 9.7 52995 52995 10.4
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.1 1.12 100 0.381 3.5 2642
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-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 1SKG 1.1 37.01 52429 529 100 0.16844 0.16826 0.18532 RANDOM 13.854
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] 0.13 0.13 -0.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.83 r_scangle_it 2.738 r_sphericity_free 2.517 r_sphericity_bonded 2.403 r_scbond_it 1.808 r_mcangle_it 1.645 r_angle_refined_deg 1.519 r_mcbond_it 1.008 r_rigid_bond_restr 0.939 r_angle_other_deg 0.774
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.83 r_scangle_it 2.738 r_sphericity_free 2.517 r_sphericity_bonded 2.403 r_scbond_it 1.808 r_mcangle_it 1.645 r_angle_refined_deg 1.519 r_mcbond_it 1.008 r_rigid_bond_restr 0.939 r_angle_other_deg 0.774 r_nbd_refined 0.425 r_nbd_other 0.241 r_symmetry_vdw_refined 0.238 r_symmetry_vdw_other 0.225 r_xyhbond_nbd_refined 0.175 r_symmetry_hbond_refined 0.174 r_nbtor_other 0.086 r_chiral_restr 0.078 r_bond_refined_d 0.009 r_gen_planes_other 0.009 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_nbtor_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_mcbond_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 993 Nucleic Acid Atoms Solvent Atoms 197 Heterogen Atoms 15
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing