☰ Navigation Tabs
X-ray structure of acidic phospholipase A2 from Indian saw-scaled viper (Echis carinatus) with a potent platelet aggregation inhibitory activity
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1CL5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.5 296 50mM Ammonium acetate, 10mM Calcium chloride, 55% ethanol, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 296K
Crystal Properties Matthews coefficient Solvent content 2.14 41.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.963 α = 90 b = 57.876 β = 90 c = 33.682 γ = 90
Symmetry Space Group P 21 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 283 IMAGE PLATE MARRESEARCH mirrors 2002-06-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU300 1.5418
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 2.6 20 97 0.098 0.098 11 11 3944 3944 -3 -3 42.4
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) 2.6 2.66 91 0.23 0.23 2.3 4 144
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 1cl5 2.6 20 3375 3375 208 95.7 0.211 0.207 0.192 0.2098 0.257 0.2917 RANDOM 33.9
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] 14.62 -8.77 -5.85
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_d 22.9 r_scangle_it 3.76 r_mcangle_it 2.43 r_scbond_it 2.41 r_mcbond_it 1.44 r_angle_deg 1.2 r_improper_angle_d 0.77 r_bond_d 0.006 r_bond_d_na r_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_d 22.9 r_scangle_it 3.76 r_mcangle_it 2.43 r_scbond_it 2.41 r_mcbond_it 1.44 r_angle_deg 1.2 r_improper_angle_d 0.77 r_bond_d 0.006 r_bond_d_na r_bond_d_prot r_angle_d r_angle_d_na r_angle_d_prot r_angle_deg_na r_angle_deg_prot r_dihedral_angle_d_na r_dihedral_angle_d_prot r_improper_angle_d_na r_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 951 Nucleic Acid Atoms Solvent Atoms 90 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling MOLREP phasing