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Crystal Structure of a New Isoform of Phospholipase A2 from Naja naja sagittifera at 1.6 A Resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1LFF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 298 sodium phosphate, ethanol, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.18 43.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.099 α = 90 b = 42.099 β = 90 c = 64.549 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 2001-09-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X11 0.80200 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 1.65 20 99 0.078 18.2 7.1 13470 12931 -3 -3 20.429
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) 1.65 1.68 99.1 0.299 3 672
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 1LFF 1.65 20 13470 12931 539 100 0.1855 0.18558 0.18408 0.22193 RANDOM 20.147
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] -0.25 -0.25 0.5
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.869 r_scangle_it 3.548 r_dihedral_angle_1_deg 3.393 r_scbond_it 2.33 r_angle_refined_deg 1.491 r_mcangle_it 1.472 r_angle_other_deg 0.973 r_mcbond_it 0.744 r_nbd_refined 0.267 r_symmetry_vdw_other 0.242
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.869 r_scangle_it 3.548 r_dihedral_angle_1_deg 3.393 r_scbond_it 2.33 r_angle_refined_deg 1.491 r_mcangle_it 1.472 r_angle_other_deg 0.973 r_mcbond_it 0.744 r_nbd_refined 0.267 r_symmetry_vdw_other 0.242 r_symmetry_vdw_refined 0.234 r_symmetry_hbond_refined 0.218 r_nbd_other 0.199 r_xyhbond_nbd_refined 0.136 r_chiral_restr 0.088 r_bond_refined_d 0.008 r_gen_planes_refined 0.004 r_gen_planes_other 0.003 r_bond_other_d 0.001 r_nbtor_other r_xyhbond_nbd_other r_symmetry_hbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 910 Nucleic Acid Atoms Solvent Atoms 148 Heterogen Atoms 6
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling AMoRE phasing REFMAC refinement