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Crystal structure of Lys49-Phospholipase A2 from Agkistrodon contortrix laticinctus, second fatty acid free form
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 291 TRIS-HCl, ammonium sulfate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.5 49.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.57 α = 90 b = 70.57 β = 90 c = 57.45 γ = 90
Symmetry Space Group P 41 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 100 IMAGE PLATE MAR scanner 345 mm plate mirror 2002-10-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU ULTRAX 18 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 1.609 26.631 99.8 0.061 0.061 49.5 14.6 35913 19354
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 1.609 1.65 99.8 0.314 0.314 8.1 14.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) 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 Sulfur-SAD at CuKa wavelength THROUGHOUT 1.609 26.63 19354 18361 991 100 0.1867 0.18577 0.1936 0.20531 0.2227 RANDOM 15.416
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] -0.17 -0.17 0.34
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.151 r_scangle_it 2.962 r_scbond_it 1.813 r_angle_refined_deg 1.295 r_mcangle_it 1.144 r_angle_other_deg 0.816 r_mcbond_it 0.619 r_symmetry_hbond_refined 0.452 r_symmetry_vdw_other 0.246 r_nbd_other 0.235
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.151 r_scangle_it 2.962 r_scbond_it 1.813 r_angle_refined_deg 1.295 r_mcangle_it 1.144 r_angle_other_deg 0.816 r_mcbond_it 0.619 r_symmetry_hbond_refined 0.452 r_symmetry_vdw_other 0.246 r_nbd_other 0.235 r_nbd_refined 0.209 r_xyhbond_nbd_refined 0.164 r_symmetry_vdw_refined 0.148 r_nbtor_other 0.083 r_chiral_restr 0.076 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 r_gen_planes_other 0.005 r_bond_other_d 0.002 r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_nbtor_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 972 Nucleic Acid Atoms Solvent Atoms 155 Heterogen Atoms 5
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling SHELXD phasing SHARP phasing ARP/wARP model building