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Crystal structure of human secreted phospholipase A2 group IIE with Compound 24
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 3.34 63.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.627 α = 90 b = 60.469 β = 90 c = 63.499 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 2014-09-29 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 2.2 18.48 99.8 0.097 0.102 0.032 0.998 20.2 9.9 9973
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 2.2 2.27 100 0.412 0.436 0.14 0.956 9.4
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5WZM 2.2 18.48 9489 473 99.69 0.1974 0.1954 0.2366 0.215 RANDOM 29.379
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] -0.05 1.47 -1.42
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.85 r_dihedral_angle_4_deg 21.478 r_dihedral_angle_3_deg 15.429 r_dihedral_angle_1_deg 5.519 r_angle_refined_deg 1.581 r_angle_other_deg 1.029 r_chiral_restr 0.092 r_bond_refined_d 0.014 r_gen_planes_refined 0.008 r_bond_other_d 0.003
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.85 r_dihedral_angle_4_deg 21.478 r_dihedral_angle_3_deg 15.429 r_dihedral_angle_1_deg 5.519 r_angle_refined_deg 1.581 r_angle_other_deg 1.029 r_chiral_restr 0.092 r_bond_refined_d 0.014 r_gen_planes_refined 0.008 r_bond_other_d 0.003 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 971 Nucleic Acid Atoms Solvent Atoms 91 Heterogen Atoms 44
Software Software Software Name Purpose Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction CrysalisPro data reduction