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Crystal Structure of a Domain-swapped Dimer of Yeast Iso-1-cytochrome c with CYMAL5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 295 Reservior solution: 77% Ammonium Sulfate, 0.1 M Tris, pH 7.5
Protein Solution: 18 mg/mL in 75 % Ammonium Sulfate
Detergent Solution: 2.5 mM CYMAL-5 in deionized water
Mixed 2:2:1
Crystal Properties Matthews coefficient Solvent content 2.6 52.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.74 α = 90 b = 69.326 β = 90 c = 72.482 γ = 90
Symmetry Space Group I 2 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE RIGAKU RAXIS IV++ Varimax-HR 2016-02-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.7 40 99.9 0.058 0.06 0.015 16 14.7 26560 26.78
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.7 1.76 99.5 0.93 0.974 0.284 0.829 11.3 2642
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION SAD, MOLECULAR REPLACEMENT FREE R-VALUE 1.701 26.981 1.34 26555 2654 99.88 0.1742 0.1708 0.1739 0.204 0.2067 38.6617
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 19.742 f_angle_d 1.04 f_chiral_restr 0.051 f_bond_d 0.009 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 843 Nucleic Acid Atoms Solvent Atoms 79 Heterogen Atoms 134
Software Software Software Name Purpose PHENIX refinement CrystalClear data collection SCALEPACK data scaling PHASER phasing SOLVE phasing PDB_EXTRACT data extraction HKL-2000 data reduction