8K6Y | pdb_00008k6y

Serial femtosecond crystallography structure of photo dissociated CO from ba3- type cytochrome c oxidase determined by extrapolation method

X-RAY DIFFRACTION

Serial Crystallography (SX)

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5NDC

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	LIPIDIC CUBIC PHASE	5.3	293	34-38 % PEG 400 (v/v), 1.4 M NaCl, pH 5.3

Crystal Properties
Matthews coefficient	Solvent content
3.3	62.69

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 145.85	α = 90
b = 100.32	β = 126.76
c = 96.62	γ = 90

Symmetry
Space Group	C 1 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	293	CCD	MPCCD		2018-02-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	FREE ELECTRON LASER	SACLA BEAMLINE BL3	0.987	SACLA	BL3

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	43.4	94.78	0.91	4	99.1		71307

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	2.071			0.55

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2	37.151	71307	1877	94.783	0.397	0.3961	0.4	0.4354	0.44	36.97

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]
-0.109		0.515	-0.684		0.011

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	17.42
r_dihedral_angle_6_deg	15.681
r_dihedral_angle_1_deg	7.699
r_dihedral_angle_2_deg	6.649
r_angle_refined_deg	1.84
r_nbtor_refined	0.318
r_nbd_refined	0.244
r_xyhbond_nbd_refined	0.241
r_symmetry_xyhbond_nbd_refined	0.223
r_symmetry_nbd_refined	0.191

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	17.42
r_dihedral_angle_6_deg	15.681
r_dihedral_angle_1_deg	7.699
r_dihedral_angle_2_deg	6.649
r_angle_refined_deg	1.84
r_nbtor_refined	0.318
r_nbd_refined	0.244
r_xyhbond_nbd_refined	0.241
r_symmetry_xyhbond_nbd_refined	0.223
r_symmetry_nbd_refined	0.191
r_chiral_restr	0.13
r_metal_ion_refined	0.101
r_bond_refined_d	0.01
r_gen_planes_refined	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5910
Nucleic Acid Atoms
Solvent Atoms	178
Heterogen Atoms	386

Software

Software
Software Name	Purpose
REFMAC	refinement
CrystFEL	data reduction
CrystFEL	data scaling
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 R01GM157729.