5NDC | pdb_00005ndc

Structure of ba3-type cytochrome c oxidase from Thermus thermophilus by serial femtosecond crystallography

X-RAY DIFFRACTION

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Serial Crystallography (SX)

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3S8F

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	LIPIDIC CUBIC PHASE	5.3	293	100mM sodium cacodylate trihydrate pH 5.3, 37% PEG400, 1.4M NaCl Room temperature for 2-3 days

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		2016-02-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	FREE ELECTRON LASER	SACLA BEAMLINE BL3	1.6314	SACLA	BL3

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	CC (Half)	R Split (All)	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	36.4	100	0.956	0.1937	3.74	14.7	1864107	50602

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	R Split (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.3	2.34			0.366	1.2		14.7

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	3S8F	2.3	36.4	47055	2511	99.92	0.1635	0.16174	0.17	0.19749	0.2	RANDOM	51.446

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]
-0.49		0.74	-1.19		0.27

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.719
r_dihedral_angle_4_deg	20.854
r_dihedral_angle_3_deg	14.321
r_dihedral_angle_1_deg	5.876
r_long_range_B_refined	4.533
r_long_range_B_other	4.533
r_scangle_other	3.138
r_mcangle_it	2.515
r_mcangle_other	2.515
r_scbond_it	1.932
r_scbond_other	1.932
r_angle_refined_deg	1.612
r_mcbond_it	1.596
r_mcbond_other	1.595
r_angle_other_deg	0.988
r_chiral_restr	0.085
r_bond_refined_d	0.012
r_gen_planes_refined	0.008
r_gen_planes_other	0.005
r_bond_other_d	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	5910
Nucleic Acid Atoms
Solvent Atoms	92
Heterogen Atoms	384

Software

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