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G307E variant of Murine Apoptosis Inducing Factor (oxidized state)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3GD3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 30% PEG 4000,0.2 M sodium acetate, pH 8.5
Crystal Properties Matthews coefficient Solvent content 2.71 54.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.04 α = 90 b = 110.06 β = 90 c = 119.59 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 PILATUS3 S 6M 2015-12-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.97895 ESRF ID29
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim 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 3.5 48.7 99.4 0.0393 0.973 5.3 5.4 16448
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.5 3.59 99.8 0.1295 0.735 1.8 5.7 1197
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 3GD3 3.5 48.7 15590 857 99.38 0.21524 0.21175 0.2213 0.27857 0.2857 RANDOM 72.943
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] -6.89 -3.48 10.37
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.851 r_dihedral_angle_3_deg 18.818 r_dihedral_angle_4_deg 16.459 r_long_range_B_refined 8.844 r_long_range_B_other 8.844 r_scangle_other 5.835 r_mcangle_it 5.39 r_mcangle_other 5.39 r_dihedral_angle_1_deg 5.376 r_angle_other_deg 3.639
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.851 r_dihedral_angle_3_deg 18.818 r_dihedral_angle_4_deg 16.459 r_long_range_B_refined 8.844 r_long_range_B_other 8.844 r_scangle_other 5.835 r_mcangle_it 5.39 r_mcangle_other 5.39 r_dihedral_angle_1_deg 5.376 r_angle_other_deg 3.639 r_scbond_it 3.486 r_scbond_other 3.485 r_mcbond_it 3.213 r_mcbond_other 3.212 r_angle_refined_deg 1.302 r_chiral_restr 0.083 r_bond_refined_d 0.008 r_gen_planes_refined 0.004 r_gen_planes_other 0.003 r_bond_other_d 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 6955 Nucleic Acid Atoms Solvent Atoms 25 Heterogen Atoms 106
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing