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Crystal structure of human secreted phospholipase A2 group IIE with Compound 8
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5WZM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 277 2.2 M Sodium chloride, 0.1 M BIS-TRIS propane pH 7.0
Crystal Properties Matthews coefficient Solvent content 3.38 63.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.006 α = 90 b = 60.998 β = 90 c = 63.301 γ = 90
Symmetry Space Group P 21 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 110 CCD OXFORD RUBY CCD 2014-08-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE OXFORD DIFFRACTION ENHANCE ULTRA 1.5406
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 18.47 99.8 0.125 0.133 0.044 0.997 17 8.9 8871
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.39 100 0.595 0.628 0.199 0.897 9.7
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 5WZM 2.3 18.47 8433 427 99.63 0.2174 0.215 0.2189 0.2655 0.2643 RANDOM 30.86
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] -0.27 1.95 -1.68
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.612 r_dihedral_angle_4_deg 16.134 r_dihedral_angle_3_deg 14.633 r_dihedral_angle_1_deg 5.259 r_angle_refined_deg 1.36 r_angle_other_deg 0.967 r_chiral_restr 0.066 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 r_bond_other_d 0.003
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.612 r_dihedral_angle_4_deg 16.134 r_dihedral_angle_3_deg 14.633 r_dihedral_angle_1_deg 5.259 r_angle_refined_deg 1.36 r_angle_other_deg 0.967 r_chiral_restr 0.066 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 r_bond_other_d 0.003 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 971 Nucleic Acid Atoms Solvent Atoms 66 Heterogen Atoms 43
Software Software Software Name Purpose Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction CrysalisPro data reduction