6KK8

XN joint refinement of manganese catalase from Thermus Thermophilus HB27

X-RAY DIFFRACTION - NEUTRON DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.2	293	1.95 M Ammonium Sulfate d-8, 14.5v/v% ethylenglycol, 50 mM AMPSO buffer pD 9.6. Drop: 32 mg/mL of manganese catalase was mixed with equal volume of Reservoir.

Crystal Properties
Matthews coefficient	Solvent content
2.97	58.65

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 133.396	α = 90
b = 133.396	β = 90
c = 133.396	γ = 90

Symmetry
Space Group	P 21 3

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	DECTRIS PILATUS 6M	Focusing mirrors with rhodium coated silicon single crystal	2017-03-20	M	SINGLE WAVELENGTH
2	1	neutron	293			Ni-Ti supermirror neutron guide Detector: iBIXDetector type: WSF PSD (Wavelength Shift Fiber Position Sensitive Detector)	2016-12-01	L	LAUE

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-17A	0.98	Photon Factory	BL-17A
2	SPALLATION SOURCE	J-PARC MLF BEAMLINE BL-03	3-6	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	1.37	44.5	100	0.092			0.03			25.7	9.8		164892		-3	16.08
2	2.349	14.4	98.2	0.322			0.151			4.5	5.2		32509		-3	16.08

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	1.37	1.39		0.956			0.365			1.8	8.4
2	2.35	2.43		0.742			0.381			1.4	4.4

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	1.37	44.465		1.33		164816	8232	99.98		0.1228	0.1222	0.1332	Random selection
NEUTRON DIFFRACTION	MOLECULAR REPLACEMENT	2.349	14.384		-2		32494	1622	98.23		0.1536	0.1516	0.191	Random selection

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	18.388
f_dihedral_angle_d	18.388
f_angle_d	1.261
f_angle_d	1.261
f_chiral_restr	0.23
f_chiral_restr	0.23
f_bond_d	0.007
f_bond_d	0.007
f_plane_restr	0.006
f_plane_restr	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4572
Nucleic Acid Atoms
Solvent Atoms	275
Heterogen Atoms	23

Software

Software
Software Name	Purpose
PHENIX	refinement
Coot	model building

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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.