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The dynamic nature of the VDAC1 channels in bilayers: human VDAC1 at 2.7 Angstrom resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3EMN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 292 25.5% precipitant mix 4 [25% (v/v) MPD, 25% (w/v) PEG 1000, 25% (w/v) PEG 3350], 0.06 M NH4NO3, 0.1 buffer system 1 [imidazole and MES adjusted to pH 6.5]
Crystal Properties Matthews coefficient Solvent content 2.87 57.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.4 α = 90 b = 58.15 β = 94.03 c = 122.72 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 80 PIXEL DECTRIS PILATUS3 2M CRL 2017-02-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-1 0.966 ESRF MASSIF-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.74 122.42 99.1 0.068 0.082 0.999 12.16 3.195 19091 60.671
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.74 2.81 99.9 0.641 0.762 0.806 2.01 3.337
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 3emn 2.74 122.42 18130 960 99.09 0.2571 0.2555 0.2584 0.2873 0.2956 RANDOM 63.365
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] -3.97 -0.69 0.54 3.49
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.013 r_dihedral_angle_4_deg 29.819 r_dihedral_angle_3_deg 18.305 r_dihedral_angle_1_deg 7.384 r_angle_refined_deg 2.101 r_chiral_restr 0.137 r_bond_refined_d 0.02 r_gen_planes_refined 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4326 Nucleic Acid Atoms Solvent Atoms 10 Heterogen Atoms 77
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling AMoRE phasing PDB_EXTRACT data extraction