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Crystal structure of a new isoform of phospholipase A2 from russells viper at 2.1 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1SV3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.8 298 0.3M Ammonium sulphate, 30% PEG8000, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.57 52.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.53 α = 90 b = 53.53 β = 90 c = 48.414 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 291 IMAGE PLATE MAR scanner 345 mm plate Mirror 2007-01-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU300 1.54132
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 2.1 53.45 96.2 7807 7442
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.1 2.18 80.1
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 1SV3 2.1 23.94 7807 7442 361 96.37 0.2 0.16662 0.166 0.1708 0.21735 0.2143 RANDOM 27.667
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] 0.21 0.21 -0.42
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 19.226 r_scangle_it 4.328 r_dihedral_angle_1_deg 4.166 r_scbond_it 2.649 r_mcangle_it 2.033 r_angle_refined_deg 1.825 r_mcbond_it 1.068 r_angle_other_deg 0.846 r_nbd_refined 0.409 r_symmetry_vdw_other 0.272
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 19.226 r_scangle_it 4.328 r_dihedral_angle_1_deg 4.166 r_scbond_it 2.649 r_mcangle_it 2.033 r_angle_refined_deg 1.825 r_mcbond_it 1.068 r_angle_other_deg 0.846 r_nbd_refined 0.409 r_symmetry_vdw_other 0.272 r_xyhbond_nbd_refined 0.218 r_nbd_other 0.212 r_symmetry_hbond_refined 0.195 r_symmetry_vdw_refined 0.153 r_xyhbond_nbd_other 0.121 r_chiral_restr 0.102 r_bond_refined_d 0.018 r_gen_planes_refined 0.008 r_gen_planes_other 0.003 r_bond_other_d 0.001 r_dihedral_angle_2_deg r_dihedral_angle_4_deg r_nbtor_refined r_nbtor_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 932 Nucleic Acid Atoms Solvent Atoms 119 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MAR345dtb data collection DENZO data reduction SCALEPACK data scaling AMoRE phasing