8GBT | pdb_00008gbt

Time-resolve SFX structure of a photoproduct of carbon monoxide complex of bovine cytochrome c oxidase

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	2DYR

Crystallization

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

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 178.3	α = 90
b = 189	β = 90
c = 209	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	PIXEL	CS-PAD CXI-1		2016-06-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	FREE ELECTRON LASER	SLAC LCLS BEAMLINE CXI	1.321	SLAC LCLS	CXI

Serial Crystallography

Sample delivery method
Diffraction ID	Description	Sample Delivery Method
1		injection

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	1.759	32.45	100	0.859	6.92	6.9		172414

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	2.87	2.99	100		0.226

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	2.8	32.002	172414	8688	99.355	0.225	0.223	0.23	0.2687	0.27	58.179

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]
-1.65			0.949		0.701

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.052
r_dihedral_angle_3_deg	18.243
r_dihedral_angle_other_3_deg	16.272
r_dihedral_angle_4_deg	15.967
r_lrange_it	9.789
r_lrange_other	9.789
r_dihedral_angle_1_deg	7.345
r_scangle_it	6.493
r_scangle_other	6.493
r_mcangle_it	6.053
r_mcangle_other	6.053
r_scbond_it	3.927
r_scbond_other	3.927
r_mcbond_it	3.717
r_mcbond_other	3.716
r_angle_refined_deg	1.553
r_angle_other_deg	1.13
r_nbd_refined	0.217
r_symmetry_nbd_refined	0.215
r_symmetry_nbd_other	0.18
r_nbtor_refined	0.175
r_xyhbond_nbd_refined	0.163
r_nbd_other	0.16
r_symmetry_xyhbond_nbd_refined	0.13
r_symmetry_xyhbond_nbd_other	0.101
r_symmetry_nbtor_other	0.083
r_chiral_restr	0.072
r_metal_ion_refined	0.059
r_bond_refined_d	0.006
r_gen_planes_refined	0.006
r_gen_planes_other	0.003
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	28488
Nucleic Acid Atoms
Solvent Atoms	245
Heterogen Atoms	2248

Software

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