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Crystal structure of Lys49-Phospholipase A2 from Agkistrodon contortrix laticinctus, first fatty acid free form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1S8G
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 = 70.505 α = 90 b = 70.505 β = 90 c = 57.146 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 2002-02-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON LNLS BEAMLINE D03B-MX1 1.544 LNLS D03B-MX1
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 1.8 19.537 97.5 0.059 0.059 8.3 3.9 13416 13416
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 1.8 1.89 99.6 0.361 0.361 2 3.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) 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 MOLECULAR REPLACEMENT THROUGHOUT 1.8 19.537 12745 670 96.71 0.19268 0.19084 0.2019 0.22886 0.239 RANDOM 20.917
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] -0.66 -0.66 1.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.086 r_scangle_it 2.24 r_scbond_it 1.337 r_angle_refined_deg 1.098 r_mcangle_it 0.86 r_angle_other_deg 0.78 r_mcbond_it 0.435 r_symmetry_vdw_other 0.252 r_nbd_other 0.213 r_nbd_refined 0.196
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.086 r_scangle_it 2.24 r_scbond_it 1.337 r_angle_refined_deg 1.098 r_mcangle_it 0.86 r_angle_other_deg 0.78 r_mcbond_it 0.435 r_symmetry_vdw_other 0.252 r_nbd_other 0.213 r_nbd_refined 0.196 r_symmetry_vdw_refined 0.144 r_xyhbond_nbd_refined 0.12 r_symmetry_hbond_refined 0.108 r_nbtor_other 0.081 r_chiral_restr 0.065 r_bond_refined_d 0.007 r_gen_planes_refined 0.004 r_gen_planes_other 0.003 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 973 Nucleic Acid Atoms Solvent Atoms 139 Heterogen Atoms 5
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction CCP4 data scaling MOLREP phasing