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Crystal structure of Lys49-Phospholipase A2 from Agkistrodon contortrix laticinctus, fatty acid bound form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1PPA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 291 cacodylate, ammonium sulfate, PEG 8000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 3 58.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.897 α = 90 b = 81.897 β = 90 c = 49.902 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 2001-10-11 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 2.3 57.3 98.1 0.118 0.118 6.2 7960 7960 1.7
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 2.3 2.41 99.7 0.118 0.118 1.7 6.2
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 (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 1PPA 2.3 57.3 7387 356 97.29 0.20663 0.20457 0.2155 0.24721 0.2494 RANDOM 41.135
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] -1.72 -1.72 3.45
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 4.673 r_scangle_it 1.169 r_angle_refined_deg 0.929 r_angle_other_deg 0.726 r_scbond_it 0.672 r_mcangle_it 0.491 r_mcbond_it 0.247 r_symmetry_vdw_other 0.225 r_nbd_other 0.194 r_nbd_refined 0.169
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 4.673 r_scangle_it 1.169 r_angle_refined_deg 0.929 r_angle_other_deg 0.726 r_scbond_it 0.672 r_mcangle_it 0.491 r_mcbond_it 0.247 r_symmetry_vdw_other 0.225 r_nbd_other 0.194 r_nbd_refined 0.169 r_symmetry_vdw_refined 0.146 r_xyhbond_nbd_refined 0.131 r_symmetry_hbond_refined 0.131 r_nbtor_other 0.082 r_chiral_restr 0.051 r_bond_refined_d 0.005 r_bond_other_d 0.002 r_gen_planes_refined 0.002 r_gen_planes_other 0.001 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 78 Heterogen Atoms 25
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction CCP4 data scaling MOLREP phasing