7YL8 | pdb_00007yl8

Neutron structure of Bacillus thermoproteolyticus Ferredoxin at room temperature

X-RAY DIFFRACTION - NEUTRON DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	MICRODIALYSIS		277	MES, ammonium sulfate

Crystal Properties
Matthews coefficient	Solvent content
2.41	49.06

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 70.43	α = 90
b = 37.91	β = 105.96
c = 33.01	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	297	CCD	ADSC QUANTUM 270		2018-12-10	M	SINGLE WAVELENGTH
2	1	neutron	297	DIFFRACTOMETER	iBIX		2018-11-02	L	LAUE

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE AR-NW12A	1.0	Photon Factory	AR-NW12A
2	SPALLATION SOURCE	J-PARC MLF BEAMLINE BL-03	1.5-4.5	JPARC MLF	BL-03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	R Split (All)	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	1.45	50	100					0.999		25.2	6.7		15007			16.15
2	1.6	15.87	99.6	0.1976	0.0685					5.15	7.5617		84041			16.15

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	R Merge I (Observed)	R-Sym I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	R Split (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.45	1.48						0.894
2	1.6	1.66		0.4602			0.1926

Refinement

Statistics
Diffraction ID	Structure Solution Method	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	Cut-off Sigma (F)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	1.45	33.08		1.38		14861	771	98.87		0.1399	0.139	0.14	0.1572	0.16		25.52
NEUTRON DIFFRACTION	MOLECULAR REPLACEMENT	1.6	15.12				10500		94.13			0.1624		0.1842

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	17.2996
f_angle_d	1.0652
f_chiral_restr	0.1093
f_bond_d	0.0107
f_plane_restr	0.0081

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	608
Nucleic Acid Atoms
Solvent Atoms	66
Heterogen Atoms	8

Software

Software
Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
REFMAC	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 R01GM157729.