5W97

Crystal Structure of CO-bound Cytochrome c Oxidase determined by Serial Femtosecond X-Ray Crystallography at Room Temperature

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3AG2

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	BATCH MODE	6.8	277	PEG 4000, Potassium Phosphate, decylmaltoside

Crystal Properties
Matthews coefficient	Solvent content
4.36	71.76

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 178.3	α = 90
b = 189	β = 90
c = 209	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	293	PIXEL	CS-PAD CXI-1		2016-06-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	FREE ELECTRON LASER	SLAC LCLS BEAMLINE CXI	1.3	SLAC LCLS	CXI

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	2.3	30	99.9	0.907	2.29	211		311037

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.3	2.38	99.9		0.156	0.57	36

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	3AG2	2.3	29.86	308128	2994	99.94	0.2088	0.2084	0.2516	RANDOM	50.784

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]
-0.05			0.09		-0.04

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.877
r_dihedral_angle_4_deg	17.722
r_dihedral_angle_3_deg	16.312
r_dihedral_angle_1_deg	6.96
r_angle_refined_deg	1.837
r_angle_other_deg	1.015
r_chiral_restr	0.118
r_bond_refined_d	0.013
r_gen_planes_refined	0.008
r_gen_planes_other	0.004

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.877
r_dihedral_angle_4_deg	17.722
r_dihedral_angle_3_deg	16.312
r_dihedral_angle_1_deg	6.96
r_angle_refined_deg	1.837
r_angle_other_deg	1.015
r_chiral_restr	0.118
r_bond_refined_d	0.013
r_gen_planes_refined	0.008
r_gen_planes_other	0.004
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	28506
Nucleic Acid Atoms
Solvent Atoms	1291
Heterogen Atoms	2228

Software

Software
Software Name	Purpose
REFMAC	refinement
CrystFEL	data scaling
MOSFLM	data reduction
PHASER	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.