8GTH | pdb_00008gth

Crystal strucuture of cyt c551 from anoxygenic phototrophic bacterium Roseiflexus castenholzii

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		289.15	1.5 M Lithium sulfate monohydrate 0.1 M BIS-TRIS propane pH 7.0

Crystal Properties
Matthews coefficient	Solvent content
3.05	59.64

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 71.63	α = 90
b = 71.63	β = 90
c = 349.76	γ = 90

Symmetry
Space Group	P 41 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS EIGER2 S 9M		2021-11-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL02U1	0.97991	SSRF	BL02U1

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	3.1	31.43	99.78	0.994	8.1	22.9		17547			74.97

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	3.1	3.211			0.569

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-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	3.1	31.43	17542	887	99.78	0.2417	0.24	0.2717	0.27

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]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	13.345
f_angle_d	0.604
f_chiral_restr	0.036
f_plane_restr	0.003
f_bond_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4563
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	258

Software

Software
Software Name	Purpose
PHENIX	refinement
Coot	model building
Coot	model building
xia2	data reduction
xia2	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction

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.