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Structure of an acidic Phospholipase A2 from the venom of Ophiophagus hannah at 2.1 resolution from a hemihedrally twinned crystal form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1POA PDB ENTRY 1POA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 291 3.4M 1,6-hexanediol, 0.2M magnesium chloride, 0.1M tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.32 46.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 98.06 α = 90 b = 98.06 β = 90 c = 132.39 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 AREA DETECTOR MARRESEARCH Osmic Mirror 2002-01-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.1 17 99.9 0.078 38.1 16.1 41966 41966 17.7
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.1 2.17 98.8 0.383 7.4 14 4153
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-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1POA 2.1 16.99 41938 41938 2026 99.9 0.196 0.192 0.1905 0.213 0.192 27.9
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] -3.98 1.14 -3.98 7.97
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 23.5 c_scangle_it 2.24 c_mcangle_it 1.92 c_angle_deg 1.5 c_scbond_it 1.49 c_mcbond_it 1.13 c_improper_angle_d 0.87 c_bond_d 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5473 Nucleic Acid Atoms Solvent Atoms 855 Heterogen Atoms 86
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MOLREP phasing CNS refinement