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Crystal Structures of Cadmium-binding Acidic Phospholipase A2 from the Venom of Agkistrodon halys pallas at 1.9 Resolution (crystal grown at pH 7.4)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1PSJ PDB ENTRY 1PSJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.4 293 10%(v/v) 1,4-butyldiol, 0.01M CdCl2, 0.1M Na(CH3)2AsO, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.35 47.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.27 α = 90 b = 83.27 β = 90 c = 32.8 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 293 AREA DETECTOR MARRESEARCH 2001-06-14 2 1 x-ray 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 2 1.9 25 99.9 0.068 26.2 7.7 10450 10450 0.0001 20.4
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) 1.9 1.97 100 0.369 5.7 6.9 1016
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 isomorphous difference Fourier THROUGHOUT PDB ENTRY 1PSJ 1.9 25 10434 1078 99.9 0.193 0.193 0.193 0.1896 0.21 0.2 RANDOM 25.7
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] 0.89 0.81 0.89 -1.78
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 22.6 c_scangle_it 5.08 c_scbond_it 3.16 c_mcangle_it 2.55 c_mcbond_it 1.59 c_angle_deg 1.3 c_improper_angle_d 0.83 c_bond_d 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 954 Nucleic Acid Atoms Solvent Atoms 81 Heterogen Atoms 13
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling CNS refinement CNS phasing