8GCQ | pdb_00008gcq

SFX structure of oxidized cytochrome c oxidase at 2.38 Angstrom resolution

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	7TIE

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	BATCH MODE	6.8	277	PEG4000, Sodium Phosphate, decylmaltoside

Crystal Properties
Matthews coefficient	Solvent content
4.35	71.74

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 178.6	α = 90
b = 189.5	β = 90
c = 211.1	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	CCD	RAYONIX MX340-HS		2022-04-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	FREE ELECTRON LASER	SLAC LCLS BEAMLINE MFX	1.24	SLAC LCLS	MFX

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	MESH	undefined (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	2.38	33	100	0.9746	4.6	8864.9426		285036

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	2.38	2.47			0.0472

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	THROUGHOUT	2.38	33	285036	14182	99.922	0.234	0.2322	0.23	0.2657	0.27	32.959

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]
-0.037			0.054		-0.018

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.975
r_dihedral_angle_3_deg	18.865
r_dihedral_angle_4_deg	18.432
r_lrange_it	9.742
r_lrange_other	9.691
r_dihedral_angle_1_deg	7.875
r_dihedral_angle_other_3_deg	6.401
r_mcangle_it	5.051
r_mcangle_other	5.051
r_scangle_it	4.825
r_scangle_other	4.825
r_mcbond_it	3.167
r_mcbond_other	3.167
r_scbond_it	2.958
r_scbond_other	2.958
r_angle_refined_deg	1.742
r_angle_other_deg	1.145
r_metal_ion_refined	0.385
r_symmetry_xyhbond_nbd_refined	0.271
r_xyhbond_nbd_refined	0.236
r_nbd_refined	0.234
r_symmetry_nbd_other	0.201
r_nbd_other	0.2
r_symmetry_nbd_refined	0.181
r_nbtor_refined	0.179
r_symmetry_xyhbond_nbd_other	0.107
r_symmetry_nbtor_other	0.083
r_chiral_restr	0.07
r_bond_refined_d	0.011
r_gen_planes_refined	0.007
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	28496
Nucleic Acid Atoms
Solvent Atoms	601
Heterogen Atoms	2368

Software

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