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Crystal structure of the complex formed between a group II phospholipase A2 and designed peptide inhibitor carbobenzoxy-dehydro-val-ala-arg-ser at 1.2 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, CaCl2, pH 7.00, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal Properties Matthews coefficient Solvent content 2.33 47.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.561 α = 90 b = 52.561 β = 90 c = 47.883 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 MIRRORS 2003-05-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X11 0.803 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 1.2 30 100 0.078 20.5 5.5 35175 35175 11.8
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 1.2 1.27 100 0.487 2.3
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 (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 PDB ENTRY 1SKG 1.25 29.36 35175 35175 921 100 0.189 0.187 0.187 0.1947 0.21 0.221 RANDOM 12.96
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] 0.05 0.05 -0.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.209 r_dihedral_angle_1_deg 5.099 r_scangle_it 2.329 r_angle_refined_deg 1.856 r_scbond_it 1.486 r_mcangle_it 1.227 r_angle_other_deg 1.037 r_mcbond_it 0.66 r_symmetry_vdw_refined 0.483 r_symmetry_hbond_refined 0.476
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.209 r_dihedral_angle_1_deg 5.099 r_scangle_it 2.329 r_angle_refined_deg 1.856 r_scbond_it 1.486 r_mcangle_it 1.227 r_angle_other_deg 1.037 r_mcbond_it 0.66 r_symmetry_vdw_refined 0.483 r_symmetry_hbond_refined 0.476 r_nbd_refined 0.435 r_symmetry_vdw_other 0.378 r_nbd_other 0.224 r_xyhbond_nbd_refined 0.182 r_xyhbond_nbd_other 0.148 r_chiral_restr 0.137 r_bond_refined_d 0.01 r_gen_planes_refined 0.01 r_gen_planes_other 0.005 r_bond_other_d 0.002 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 984 Nucleic Acid Atoms Solvent Atoms 199 Heterogen Atoms 15
Software Software Software Name Purpose HKL-2000 data collection AMoRE phasing REFMAC refinement DENZO data reduction SCALEPACK data scaling