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Crystal structure of the V243L mutant of human apoptosis inducing factor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5FS8 PDB ENTRY 5FS8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 0.2 M AMMONIUM ACETATE, 0.1M HEPES, PH 7.5, AND 20% POLY-ETHYLENE GLYCOL 3350
Crystal Properties Matthews coefficient Solvent content 2.81 56.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.84 α = 90 b = 114.38 β = 90 c = 121.26 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 110 CCD MARMOSAIC 325 mm CCD MIRRORS 2015-08-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL14-1 SSRL BL14-1
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 1.9 83.2 99.3 0.12 7.4 4.2 99250 2
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 1.9 2 97.8 0.79 1.6 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 PDB ENTRY 5FS8 1.9 121.26 94198 4956 99.19 0.1738 0.17206 0.20689 0.2053 RANDOM 30.855
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] -0.02 -0.1 0.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.204 r_dihedral_angle_4_deg 18.816 r_dihedral_angle_3_deg 14.286 r_dihedral_angle_1_deg 6.017 r_mcangle_it 2.255 r_scbond_it 1.999 r_angle_refined_deg 1.609 r_mcbond_it 1.419 r_mcbond_other 1.418 r_angle_other_deg 0.786
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.204 r_dihedral_angle_4_deg 18.816 r_dihedral_angle_3_deg 14.286 r_dihedral_angle_1_deg 6.017 r_mcangle_it 2.255 r_scbond_it 1.999 r_angle_refined_deg 1.609 r_mcbond_it 1.419 r_mcbond_other 1.418 r_angle_other_deg 0.786 r_chiral_restr 0.141 r_bond_refined_d 0.012 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 7008 Nucleic Acid Atoms Solvent Atoms 907 Heterogen Atoms 122
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing