5ZE8

Crystal structure of a penta-heme cytochrome c552 from Thermochromatium tepidum

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	PEG 3350, calcium chloride, ammonium chloride

Crystal Properties
Matthews coefficient	Solvent content
1.92	36.05

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 144.7	α = 90
b = 39.1	β = 109.31
c = 68.65	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	100	PIXEL	DECTRIS PILATUS3 6M		2016-12-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL41XU	1.0	SPring-8	BL41XU

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	1.6	68.28	99.94	0.999	25.02	12.9		48283

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	1.6	1.66	99.66		0.841	5.16	10.7

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	1.6	68.28	45846	2437	99.94	0.1595	0.1577	0.1908	RANDOM	20.417

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
r_dihedral_angle_2_deg	33.059
r_dihedral_angle_4_deg	25.626
r_dihedral_angle_3_deg	14.806
r_dihedral_angle_1_deg	6.538
r_angle_refined_deg	2.261
r_angle_other_deg	1.292
r_chiral_restr	0.165
r_bond_refined_d	0.023
r_gen_planes_refined	0.018
r_gen_planes_other	0.018

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.059
r_dihedral_angle_4_deg	25.626
r_dihedral_angle_3_deg	14.806
r_dihedral_angle_1_deg	6.538
r_angle_refined_deg	2.261
r_angle_other_deg	1.292
r_chiral_restr	0.165
r_bond_refined_d	0.023
r_gen_planes_refined	0.018
r_gen_planes_other	0.018
r_bond_other_d	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2975
Nucleic Acid Atoms
Solvent Atoms	351
Heterogen Atoms	226

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
XDS	data scaling
SHELXDE	phasing

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 R01GM133198.