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Crystal Structure of Russelles viper (Daboia russellii pulchella) phospholipase A2 in a complex with venom 6-methyl heptanol
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1FVO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 298 0.1M Cacodylate buffer, 0.2M Ammonoum Sulphate, 15% PEG8000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.19 43.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.866 α = 90 b = 69.071 β = 90 c = 75.646 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 291 IMAGE PLATE MARRESEARCH Monochromator 2002-09-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200 1.5418
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 2.4 20 98.1 0.072 25.2 7.3 58251 7984 18.9
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) 2.4 2.5 95.3 0.31 3.2
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-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1FVO 2.45 19.86 7345 7345 390 79.1 0.195 0.192 0.192 0.235 RANDOM 27.3
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]
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 24.1 c_scangle_it 4.72 c_mcangle_it 3.27 c_scbond_it 3.18 c_angle_deg 2.8 c_mcbond_it 2.04 c_improper_angle_d 1.17 c_bond_d 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1892 Nucleic Acid Atoms Solvent Atoms 148 Heterogen Atoms 27
Software Software Software Name Purpose CNS refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing