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Structure-based rational drug design: Crystal structure of the complex formed between Phospholipase A2 and a pentapeptide Val-Ala-Phe-Arg-Ser
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1FB2
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 298.0K
Crystal Properties Matthews coefficient Solvent content 2.5 49.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.35 α = 90 b = 52.35 β = 90 c = 47.828 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 2003-09-29 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 20 99.5 0.078 16.6 9.9 393280 39363 12.4
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) 1.2 1.23 97.9 0.428 4.8
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 1FB2 1.21 20 38357 38357 990 97 0.1464 0.1433 0.141 0.1833 RANDOM 18.5
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]
Coordinate Error Structure Solution Method Refinement High Resolution Refinement Low Resolution 1244.5
RMS Deviations Key Refinement Restraint Deviation s_non_zero_chiral_vol 0.078 s_zero_chiral_vol 0.068 s_approx_iso_adps 0.061 s_similar_adp_cmpnt 0.049 s_anti_bump_dis_restr 0.038 s_angle_d 0.03 s_from_restr_planes 0.0286 s_bond_d 0.013 s_rigid_bond_adp_cmpnt 0.005 s_similar_dist
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 984 Nucleic Acid Atoms Solvent Atoms 254 Heterogen Atoms 20
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling SHELX model building SHELXL-97 refinement AMoRE phasing