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Crystal structure of the complex formed between group II phospholipase A2 with a designed pentapeptide, Phe- Leu- Ser- Thr- Lys 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, SITTING DROP 6 293 Ammonium Sulphate, Polyethylene glycol, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.4 47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.293 α = 90 b = 52.293 β = 90 c = 47.83 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 2004-04-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X11 0.8030 EMBL/DESY, HAMBURG X11
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 1.25 20 100 35680 35680
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.25 1.28 99
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-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT pdb entry 1SKG 1.25 51.99 35680 34764 916 99.98 0.18454 0.18406 0.20273 RANDOM 14.014
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] 0.04 0.04 -0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.488 r_dihedral_angle_1_deg 4.769 r_scangle_it 2.257 r_angle_refined_deg 1.725 r_scbond_it 1.461 r_mcangle_it 1.183 r_angle_other_deg 0.751 r_mcbond_it 0.625 r_nbd_refined 0.426 r_symmetry_vdw_other 0.285
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.488 r_dihedral_angle_1_deg 4.769 r_scangle_it 2.257 r_angle_refined_deg 1.725 r_scbond_it 1.461 r_mcangle_it 1.183 r_angle_other_deg 0.751 r_mcbond_it 0.625 r_nbd_refined 0.426 r_symmetry_vdw_other 0.285 r_xyhbond_nbd_refined 0.239 r_symmetry_vdw_refined 0.238 r_nbd_other 0.215 r_symmetry_hbond_refined 0.205 r_chiral_restr 0.088 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 982 Nucleic Acid Atoms Solvent Atoms 232 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement MAR345 data collection SCALEPACK data scaling AMoRE phasing