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Lysine-Ligated Yeast Iso-1 Cytochrome C
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1YEA PDB ENTRY 1YEA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 291 0.2 M ammonium phosphate, pH 8.1, 30% w/v PEG300, 0.1 M Tris, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 3.07 59.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 106.02 α = 90 b = 106.02 β = 90 c = 149.84 γ = 90
Symmetry Space Group I 4 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 CCD ADSC QUANTUM 270 2013-10-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X6A 1.0781 NSLS X6A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.87 19.52 99.9 0.072 0.07 29.96 35597 35544 7 29.96
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.87 1.97 99.9 0.597 0.567 4.3
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 1YEA 1.87 19.52 33766 1777 99.8 0.17386 0.17228 0.1767 0.20367 0.2069 RANDOM 28.213
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] -3.93 -3.93 7.85
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.52 r_dihedral_angle_3_deg 21.07 r_dihedral_angle_4_deg 13.514 r_dihedral_angle_1_deg 7.329 r_mcangle_it 5.065 r_scbond_it 4.491 r_mcbond_it 4.122 r_mcbond_other 4.107 r_angle_other_deg 3.548 r_angle_refined_deg 1.228
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.52 r_dihedral_angle_3_deg 21.07 r_dihedral_angle_4_deg 13.514 r_dihedral_angle_1_deg 7.329 r_mcangle_it 5.065 r_scbond_it 4.491 r_mcbond_it 4.122 r_mcbond_other 4.107 r_angle_other_deg 3.548 r_angle_refined_deg 1.228 r_chiral_restr 0.155 r_gen_planes_other 0.049 r_gen_planes_refined 0.021 r_bond_refined_d 0.009 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_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 2423 Nucleic Acid Atoms Solvent Atoms 86 Heterogen Atoms 129
Software Software Software Name Purpose REFMAC refinement PHENIX model building PHENIX refinement XDS data reduction XSCALE data scaling PHENIX phasing HKL-2000 data collection