8HUA | pdb_00008hua

Serial synchrotron crystallography structure of ba3-type cytochrome c oxidase from Thermus thermophilus using a goniometer compatible flow-cell

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	5NDC

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	LIPIDIC CUBIC PHASE	5.3	298	1.4 M NaCl, 100 mM MES pH 5.3 with 36 % to 39 % (v/v) PEG 400

Crystal Properties
Matthews coefficient	Solvent content
3.3	62.69

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 146.06	α = 90
b = 100.17	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	298	PIXEL	DECTRIS EIGER X 16M		2019-12-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	MAX IV BEAMLINE BioMAX	0.98	MAX IV	BioMAX

Serial Crystallography

Sample delivery method
Diffraction ID	Description	Sample Delivery Method
1		injection

Injection
Diffraction ID	Description	Flow Rate	Injector Diameter	Injection Power	Injector Nozzle	Filter Size	Carrier Solvent
1	Capillary-based flow-cell	1.2 (µl/min)	undefined (µm)

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	2.12	25.802	100	0.99	6.8	123.6		65010

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	2.12	2.2			0.52

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	2.12	25.802	63185	3207	99.932	0.154	0.152	0.16	0.1844	0.19	48.819

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]
0.014		0.007	-0.016		-0.004

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.985
r_dihedral_angle_4_deg	21.384
r_dihedral_angle_3_deg	14.473
r_lrange_it	8.128
r_lrange_other	8.128
r_scangle_it	6.886
r_scangle_other	6.885
r_dihedral_angle_1_deg	6.262
r_mcangle_it	4.861
r_mcangle_other	4.861
r_scbond_it	4.689
r_scbond_other	4.688
r_mcbond_it	3.664
r_mcbond_other	3.662
r_angle_refined_deg	1.72
r_angle_other_deg	1.276
r_symmetry_nbd_refined	0.272
r_symmetry_xyhbond_nbd_refined	0.222
r_nbd_refined	0.221
r_nbd_other	0.188
r_symmetry_nbd_other	0.178
r_nbtor_refined	0.174
r_xyhbond_nbd_refined	0.13
r_metal_ion_refined	0.12
r_chiral_restr	0.083
r_symmetry_nbtor_other	0.079
r_bond_refined_d	0.009
r_gen_planes_refined	0.009
r_gen_planes_other	0.006
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5910
Nucleic Acid Atoms
Solvent Atoms	104
Heterogen Atoms	384

Software

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