☰ Navigation Tabs
Crystal structure of phospholipase A2 ammodytoxin A from vipera ammodytes ammodytes
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ZWP PDB ENTRY 1ZWP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 291 1.26M (NH4)2SO4, 0.1M TRIS, 0.2M (LI)2SO4, pH 8.50, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.24 45.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.19 α = 90 b = 68.19 β = 90 c = 46.08 γ = 120
Symmetry Space Group P 3 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 110 CCD MARMOSAIC 225 mm CCD MIRROR 2007-03-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 0.8726 ESRF ID23-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.7 29.527 99.9 0.143 0.143 4.7 10.4 13933 13933 -3 14.39
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.7 1.79 99.7 0.791 0.791 1 10.2
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 PDB ENTRY 1ZWP 1.7 29.527 13933 13933 531 99.9 0.174 0.174 0.172 0.1812 0.216 0.2227 RANDOM 12.71
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] -0.7 -0.35 -0.7 1.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.632 r_dihedral_angle_4_deg 17.323 r_dihedral_angle_3_deg 12.785 r_dihedral_angle_1_deg 4.554 r_scangle_it 2.718 r_scbond_it 2 r_mcangle_it 1.697 r_mcbond_it 1.367 r_angle_refined_deg 1.193 r_angle_other_deg 0.825
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.632 r_dihedral_angle_4_deg 17.323 r_dihedral_angle_3_deg 12.785 r_dihedral_angle_1_deg 4.554 r_scangle_it 2.718 r_scbond_it 2 r_mcangle_it 1.697 r_mcbond_it 1.367 r_angle_refined_deg 1.193 r_angle_other_deg 0.825 r_mcbond_other 0.272 r_nbd_refined 0.219 r_symmetry_vdw_refined 0.203 r_symmetry_hbond_refined 0.185 r_nbtor_refined 0.182 r_symmetry_vdw_other 0.174 r_nbd_other 0.172 r_xyhbond_nbd_refined 0.17 r_nbtor_other 0.084 r_chiral_restr 0.067 r_bond_refined_d 0.012 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 957 Nucleic Acid Atoms Solvent Atoms 151 Heterogen Atoms 5
Software Software Software Name Purpose XDS data scaling PHASER phasing REFMAC refinement XDS data reduction SCALA data scaling