Experiment: 6KK8

XN joint refinement of manganese catalase from Thermus Thermophilus HB27

X-RAY DIFFRACTION - NEUTRON DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2V8U

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	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	0.1223	0.1332	0.1328	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

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