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Crystal structure of human secreted phospholipase A2 group IIE with Compound 14
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 2.2M Sodium chloride, 0.1M BIS-TRIS propane pH 7.0
Crystal Properties Matthews coefficient Solvent content 3.36 63.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.93 α = 90 b = 60.676 β = 90 c = 63.379 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 2014-09-25 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 2.4 18.47 99.8 0.123 0.13 0.042 0.997 16.8 9.2 7799
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 2.4 2.49 100 0.604 0.636 0.196 0.889 10.2
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 5WZM 2.4 18.47 7405 373 99.48 0.221 0.2186 0.2246 0.2674 0.2599 RANDOM 32.773
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] -1.26 3.04 -1.78
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.108 r_dihedral_angle_3_deg 17.142 r_dihedral_angle_4_deg 15.653 r_dihedral_angle_1_deg 5.38 r_angle_refined_deg 1.421 r_angle_other_deg 0.944 r_chiral_restr 0.074 r_bond_refined_d 0.011 r_gen_planes_refined 0.007 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.108 r_dihedral_angle_3_deg 17.142 r_dihedral_angle_4_deg 15.653 r_dihedral_angle_1_deg 5.38 r_angle_refined_deg 1.421 r_angle_other_deg 0.944 r_chiral_restr 0.074 r_bond_refined_d 0.011 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 971 Nucleic Acid Atoms Solvent Atoms 50 Heterogen Atoms 39
Software Software Software Name Purpose Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction CrysalisPro data reduction