6CUN

Engineered Cytochrome c from Rhodothermus marinus (Rma TDE) bound to carbene intermediate (1-ethoxy-1-oxopropan-2-ylidene)

X-RAY DIFFRACTION

---

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	R-Free	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	0.20234	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
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