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Crystal structure of phospholipase A2 ammodytoxin C 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 8 291 1.2M (NH4)2SO4, 0.1M IMIDAZOLE, 0.2M (LI)2SO4, pH 8.00, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.18 43.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.73 α = 90 b = 67.73 β = 90 c = 45.34 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 ADSC QUANTUM 315 MIRROR 2007-01-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.97565 ESRF ID23-1
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 1.35 45.33 96.5 0.084 0.084 6.7 10 25781 25781 -3 8.7
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 1.35 1.42 79.8 0.661 0.661 1.2 6.4
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 1.35 45.33 25781 25781 1013 96.5 0.172 0.172 0.171 0.1796 0.196 0.1979 RANDOM 13.05
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] -0.88 -0.44 -0.88 1.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.369 r_dihedral_angle_4_deg 17.577 r_dihedral_angle_3_deg 13.058 r_dihedral_angle_1_deg 5.261 r_scangle_it 2.999 r_scbond_it 2.193 r_mcangle_it 1.882 r_mcbond_it 1.559 r_angle_refined_deg 1.464 r_angle_other_deg 0.881
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.369 r_dihedral_angle_4_deg 17.577 r_dihedral_angle_3_deg 13.058 r_dihedral_angle_1_deg 5.261 r_scangle_it 2.999 r_scbond_it 2.193 r_mcangle_it 1.882 r_mcbond_it 1.559 r_angle_refined_deg 1.464 r_angle_other_deg 0.881 r_mcbond_other 0.308 r_nbd_refined 0.223 r_symmetry_vdw_other 0.204 r_symmetry_vdw_refined 0.192 r_nbtor_refined 0.19 r_nbd_other 0.185 r_xyhbond_nbd_refined 0.16 r_symmetry_hbond_refined 0.117 r_nbtor_other 0.088 r_chiral_restr 0.084 r_bond_refined_d 0.013 r_gen_planes_refined 0.006 r_bond_other_d 0.002 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 954 Nucleic Acid Atoms Solvent Atoms 199 Heterogen Atoms 5
Software Software Software Name Purpose XDS data scaling PHASER phasing REFMAC refinement XDS data reduction SCALA data scaling