Experiment: 5X19

CO bound cytochrome c oxidase at 100 micro sec after pump laser irradiation to release CO from O2 reduction center

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3AG1

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	BATCH MODE	6.8	277	40 mM sodium phosphate, 0.2% decyl maltoside, 2% ethylene glycol, PEG 4000

Crystal Properties
Matthews coefficient	Solvent content
4.19	70.67

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 185.034	α = 90
b = 208.846	β = 90
c = 178.046	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	277	CCD	RAYONIX MX225HE		2015-10-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	FREE ELECTRON LASER	SACLA BEAMLINE BL3	1.23970	SACLA	BL3

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.2	25	96.9	0.1677	0.9429	11.78	70.89		336147

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.2	2.24	88.4		0.3812	0.5907		5.72

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	3AG1	2.2	25	318914	17156	96.76	0.1749	0.173	0.1737	0.2097	0.2103	RANDOM	68.013

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]
0.58			2.75		-3.33

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.493
r_dihedral_angle_3_deg	17.805
r_dihedral_angle_4_deg	17.107
r_dihedral_angle_1_deg	6.37
r_angle_refined_deg	1.975
r_chiral_restr	0.126
r_bond_refined_d	0.016
r_gen_planes_refined	0.01

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	28506
Nucleic Acid Atoms
Solvent Atoms	1415
Heterogen Atoms	2256

Software

Software
Software Name	Purpose
REFMAC	refinement
cctbx.xfel	data processing
cctbx.prime	data scaling
REFMAC	phasing