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Crystal structure of the complex of group I phospholipase A2 with 4-Methoxy-benzoicacid at 1.4A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1OXR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 293 10MM sodium phosphate buffer, 2M calcium chloride, 35% ethanol, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.17 43.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.074 α = 90 b = 42.074 β = 90 c = 64.253 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 77 CCD MARRESEARCH Mirror 2010-05-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 0.97 ESRF BM14
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 1.4 42 96.5 0.063 79.9 22095 22095 19.1
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 1.4 1.42 95 0.448 5.5
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 1OXR 1.4 19.09 22095 20236 1102 96.59 0.17742 0.17673 0.17424 0.1722 0.22388 0.2224 RANDOM 25.03
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] -0.21 -0.21 0.43
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.654 r_dihedral_angle_3_deg 13.516 r_dihedral_angle_4_deg 10.31 r_sphericity_free 7.819 r_sphericity_bonded 6.052 r_dihedral_angle_1_deg 5.855 r_scangle_it 4.602 r_mcangle_it 3.976 r_scbond_it 3.645 r_mcbond_it 3.101
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.654 r_dihedral_angle_3_deg 13.516 r_dihedral_angle_4_deg 10.31 r_sphericity_free 7.819 r_sphericity_bonded 6.052 r_dihedral_angle_1_deg 5.855 r_scangle_it 4.602 r_mcangle_it 3.976 r_scbond_it 3.645 r_mcbond_it 3.101 r_rigid_bond_restr 2.807 r_angle_refined_deg 1.693 r_nbtor_refined 0.321 r_symmetry_vdw_refined 0.318 r_symmetry_hbond_refined 0.278 r_nbd_refined 0.262 r_xyhbond_nbd_refined 0.24 r_chiral_restr 0.112 r_metal_ion_refined 0.08 r_bond_refined_d 0.017 r_gen_planes_refined 0.012 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_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 910 Nucleic Acid Atoms Solvent Atoms 286 Heterogen Atoms 12
Software Software Software Name Purpose HKL-2000 data collection AMoRE phasing REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling