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Crystal structure of the G308E mutant of human apoptosis inducing factor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1M6I PDB ENTRY 1M6I
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 0.2 M AMMONIUM ACETATE AND 20% POLY-ETHYLENE GLYCOL, pH 7.5
Crystal Properties Matthews coefficient Solvent content 2.45 49.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.79 α = 90 b = 89.75 β = 94.93 c = 60.33 γ = 90
Symmetry Space Group P 1 21 1
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 2012-07-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 SSRL BL9-2
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 1.4 37.17 97.1 0.06 9.4 3.6 102452 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 1.4 1.48 88.7 0.62 1.5 2.9
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 PDB ENTRY 1M6I 1.4 89.75 97342 5075 96.81 0.16583 0.16443 0.1733 0.19247 0.1968 RANDOM 23.382
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] 1.09 -0.41 0.55 -1.54
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.201 r_dihedral_angle_4_deg 19.351 r_dihedral_angle_3_deg 12.343 r_dihedral_angle_1_deg 5.829 r_scangle_it 2.663 r_mcangle_it 1.997 r_scbond_it 1.641 r_angle_refined_deg 1.541 r_mcbond_it 1.216 r_mcbond_other 1.216
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.201 r_dihedral_angle_4_deg 19.351 r_dihedral_angle_3_deg 12.343 r_dihedral_angle_1_deg 5.829 r_scangle_it 2.663 r_mcangle_it 1.997 r_scbond_it 1.641 r_angle_refined_deg 1.541 r_mcbond_it 1.216 r_mcbond_other 1.216 r_angle_other_deg 0.783 r_chiral_restr 0.088 r_bond_refined_d 0.011 r_gen_planes_refined 0.008 r_gen_planes_other 0.002 r_bond_other_d 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_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 3665 Nucleic Acid Atoms Solvent Atoms 644 Heterogen Atoms 53
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing