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Crystal structure of human PLA2G5 in complex with a SMOL inhibitor (compound 1)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other internal model
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 9 295 100 mM Bicine pH 9.0, 2.0 M MgCl2
Crystal Properties Matthews coefficient Solvent content 2.21 44.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.99 α = 90 b = 67.29 β = 90 c = 68.32 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M-F 2016-06-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9795 Diamond I04
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 2.49 30.46 98 0.153 0.167 0.066 0.996 8.1 6.3 8832 30.8
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 2.49 2.55 96.5 0.826 0.897 0.346 0.89 6.6
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 2.49 30.46 8405 399 97.92 0.26235 0.25957 0.2811 0.31969 0.3559 RANDOM 44.864
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] -6.48 10.68 -4.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.949 r_dihedral_angle_4_deg 19.906 r_dihedral_angle_3_deg 16.696 r_long_range_B_refined 8.806 r_long_range_B_other 8.796 r_dihedral_angle_1_deg 7.049 r_scangle_other 5.171 r_mcangle_it 4.538 r_mcangle_other 4.536 r_scbond_it 3.072
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.949 r_dihedral_angle_4_deg 19.906 r_dihedral_angle_3_deg 16.696 r_long_range_B_refined 8.806 r_long_range_B_other 8.796 r_dihedral_angle_1_deg 7.049 r_scangle_other 5.171 r_mcangle_it 4.538 r_mcangle_other 4.536 r_scbond_it 3.072 r_scbond_other 3.071 r_mcbond_it 2.856 r_mcbond_other 2.855 r_angle_refined_deg 1.473 r_angle_other_deg 1.001 r_chiral_restr 0.083 r_bond_refined_d 0.011 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1908 Nucleic Acid Atoms Solvent Atoms 42 Heterogen Atoms 45
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction PHASER phasing