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Ether Lipid-Generating Enzyme AGPS in complex with antimycin A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4BBY PDB ENTRY 4BBY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 PH 7.5
Crystal Properties Matthews coefficient Solvent content 2.22 44.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.159 α = 90.8 b = 98.85 β = 90.5 c = 107.722 γ = 94.79
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 2014-04-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23 ESRF ID23
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.18 34.67 94.2 0.1 7 3.4 123594
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.18 2.22 93.1 0.7 1.9 3.6
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 PDB ENTRY 4BBY 2.18 107.71 122248 1333 94.19 0.19209 0.19139 0.2588 0.2773 RANDOM 37.86
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] -0.14 0.25 -0.19 -0.8 -1.37 0.96
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.005 r_dihedral_angle_4_deg 18.298 r_dihedral_angle_3_deg 16.018 r_dihedral_angle_1_deg 6.96 r_mcangle_it 4.159 r_scbond_it 3.491 r_mcbond_it 2.878 r_mcbond_other 2.878 r_angle_refined_deg 1.79 r_angle_other_deg 1.045
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.005 r_dihedral_angle_4_deg 18.298 r_dihedral_angle_3_deg 16.018 r_dihedral_angle_1_deg 6.96 r_mcangle_it 4.159 r_scbond_it 3.491 r_mcbond_it 2.878 r_mcbond_other 2.878 r_angle_refined_deg 1.79 r_angle_other_deg 1.045 r_chiral_restr 0.1 r_bond_refined_d 0.016 r_gen_planes_refined 0.008 r_bond_other_d 0.003 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_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 17118 Nucleic Acid Atoms Solvent Atoms 589 Heterogen Atoms 383
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction Aimless data scaling PHASER phasing