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Crystal Structure of the complex formed between group II phospholipase A2 and a plant alkaloid ajmaline at 2.0A 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, SITTING DROP 7 298 0.2M AMMONIUM SULPHATE, 30% PEG, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.5 50
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.257 α = 90 b = 53.257 β = 90 c = 48.657 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 300 IMAGE PLATE MARRESEARCH mirror 2005-04-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU300 1.5418
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 2.03 54.5 98 0.077 10.9 67845 8322 32.9
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) 2.03 2.12 94.1 0.528 2.8
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-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1SKG 2.03 20 8307 8307 419 98.12 0.1896 0.1896 0.18596 0.22146 RANDOM 25.475
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 14.454 r_angle_refined_deg 3.925 r_scangle_it 3.601 r_scbond_it 2.314 r_dihedral_angle_1_deg 2.019 r_mcangle_it 1.9 r_angle_other_deg 1.402 r_nbtor_other 1.033 r_mcbond_it 0.994 r_nbd_refined 0.447
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.454 r_angle_refined_deg 3.925 r_scangle_it 3.601 r_scbond_it 2.314 r_dihedral_angle_1_deg 2.019 r_mcangle_it 1.9 r_angle_other_deg 1.402 r_nbtor_other 1.033 r_mcbond_it 0.994 r_nbd_refined 0.447 r_chiral_restr 0.342 r_symmetry_vdw_refined 0.278 r_xyhbond_nbd_other 0.256 r_nbd_other 0.243 r_xyhbond_nbd_refined 0.226 r_symmetry_vdw_other 0.213 r_symmetry_hbond_refined 0.212 r_symmetry_hbond_other 0.051 r_gen_planes_other 0.035 r_gen_planes_refined 0.03 r_bond_refined_d 0.014 r_bond_other_d 0.003 r_dihedral_angle_2_deg r_dihedral_angle_4_deg r_nbtor_refined r_metal_ion_refined r_metal_ion_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 944 Nucleic Acid Atoms Solvent Atoms 114 Heterogen Atoms 32
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing