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Crystal Structure of Phospholipase A2 complex with propanol at 1.5 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2OYF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.8 300 0.2M ammonium sulphate, 30% PEG 4000, pH 6.8, VAPOR DIFFUSION, SITTING DROP, temperature 300K
Crystal Properties Matthews coefficient Solvent content 2.37 48.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.15 α = 90 b = 52.15 β = 90 c = 47.611 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 CCD MAR CCD 165 mm mirror 2007-03-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X11 0.9012 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 1.5 25 100 0.046 60.2 41.6 20479 20479 22.2
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) 1.5 1.53 99.8 0.534 6.1
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 2OYF 1.5 25 20479 19431 1048 99.45 0.19232 0.19199 0.19128 0.1936 0.20533 0.2094 RANDOM 27.201
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] 0.3 0.3 -0.6
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.411 r_dihedral_angle_3_deg 12.91 r_dihedral_angle_4_deg 8 r_dihedral_angle_1_deg 5.475 r_scangle_it 3.22 r_scbond_it 2.125 r_mcangle_it 1.672 r_angle_refined_deg 1.385 r_mcbond_it 1.041 r_nbd_refined 0.347
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.411 r_dihedral_angle_3_deg 12.91 r_dihedral_angle_4_deg 8 r_dihedral_angle_1_deg 5.475 r_scangle_it 3.22 r_scbond_it 2.125 r_mcangle_it 1.672 r_angle_refined_deg 1.385 r_mcbond_it 1.041 r_nbd_refined 0.347 r_nbtor_refined 0.308 r_xyhbond_nbd_refined 0.206 r_symmetry_vdw_refined 0.16 r_symmetry_hbond_refined 0.118 r_chiral_restr 0.079 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_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 944 Nucleic Acid Atoms Solvent Atoms 204 Heterogen Atoms 24
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction SCALEPACK data scaling AMoRE phasing