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Crystal structure of the complex of group II phospholipase A2 with Eugenol
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ZR8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 298 0.2M AMMONIUM SULPHATE, 30% PEG 4000, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.47 50.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.795 α = 90 b = 52.795 β = 90 c = 48.397 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 2007-07-25 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 2.08 52.78 96.7 0.116 9.75 8128 8128
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) 2.08 2.15 84 0.366 1.51
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 1ZR8 2.08 52.78 8128 7472 362 96.73 0.17781 0.17668 0.17471 0.2171 RANDOM 36.082
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] 0.42 0.42 -0.83
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.906 r_dihedral_angle_4_deg 20.389 r_dihedral_angle_3_deg 19.274 r_dihedral_angle_1_deg 6.205 r_scangle_it 4.68 r_scbond_it 3.02 r_mcangle_it 2.139 r_angle_refined_deg 1.843 r_mcbond_it 1.264 r_nbd_refined 0.362
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.906 r_dihedral_angle_4_deg 20.389 r_dihedral_angle_3_deg 19.274 r_dihedral_angle_1_deg 6.205 r_scangle_it 4.68 r_scbond_it 3.02 r_mcangle_it 2.139 r_angle_refined_deg 1.843 r_mcbond_it 1.264 r_nbd_refined 0.362 r_nbtor_refined 0.312 r_symmetry_vdw_refined 0.255 r_xyhbond_nbd_refined 0.207 r_symmetry_hbond_refined 0.204 r_chiral_restr 0.106 r_bond_refined_d 0.02 r_gen_planes_refined 0.008 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 73 Heterogen Atoms 16
Software Software Software Name Purpose REFMAC refinement DENZO data reduction AUTOMAR data reduction SCALEPACK data scaling AMoRE phasing