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Engineered Cytochrome c from Rhodothermus marinus (Rma TDE) bound to carbene intermediate (1-ethoxy-1-oxopropan-2-ylidene)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6CUK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 1.43-1.48 M (NH4)2SO4
300-400 mM NaSCN
1.5% isopropanol
2:1 ratio of Rma TDE (14 mg/mL in 20mM Tris HCl pH 7.5) to well solution
Crystals were soaked in well solution supplemented with 40 mM ethyl 2-diazopropanoate under aerobic conditions for 30 minutes, followed by addition of sodium dithionite (50 mM) and freezing with liquid nitrogen
Crystal Properties Matthews coefficient Solvent content 2.89 57.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.343 α = 90 b = 60.343 β = 90 c = 77.232 γ = 120
Symmetry Space Group P 32 2 1
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 PILATUS 6M 2017-07-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-2 0.97946 SSRL BL12-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.29 38.62 100 21.4 19.4 39554
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.29 1.32 100 2.9 16.6
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 6CUK 1.29 38.62 39554 1935 99.97 0.18192 0.18095 0.1899 0.20234 0.207 RANDOM 22.775
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] 0.52 0.26 0.52 -1.7
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.652 r_dihedral_angle_4_deg 18.403 r_dihedral_angle_3_deg 10.721 r_dihedral_angle_1_deg 6.653 r_long_range_B_refined 5.108 r_long_range_B_other 4.928 r_angle_refined_deg 1.814 r_scangle_other 1.791 r_mcangle_it 1.43 r_mcangle_other 1.429
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.652 r_dihedral_angle_4_deg 18.403 r_dihedral_angle_3_deg 10.721 r_dihedral_angle_1_deg 6.653 r_long_range_B_refined 5.108 r_long_range_B_other 4.928 r_angle_refined_deg 1.814 r_scangle_other 1.791 r_mcangle_it 1.43 r_mcangle_other 1.429 r_scbond_it 1.275 r_scbond_other 1.274 r_angle_other_deg 1.014 r_mcbond_it 0.899 r_mcbond_other 0.899 r_chiral_restr 0.108 r_bond_refined_d 0.018 r_gen_planes_refined 0.011 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 847 Nucleic Acid Atoms Solvent Atoms 100 Heterogen Atoms 50
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing