6EBD

OhrB (Organic Hydroperoxide Resistance protein) mutant (C60A) from Chromobacterium violaceum, interacting with dihydrolipoamide

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6EB4

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.5	291.15	Purified Ohr_C60A protein 10mg/ml in 5mM Tris-Hcl pH 7.4 Crystallisation conditions: Magnesium Clhoride 200mM, BIS-TRIS 100mM pH 5.5, PEG 3,350 25%w/v crystal was soaked for 10min in Lipoamide 5mM, solved in 5% ethanol and Crystallisation condition

Crystal Properties
Matthews coefficient	Solvent content
2.96	62.71

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 87.675	α = 90
b = 87.675	β = 90
c = 179.609	γ = 120

Symmetry
Space Group	P 61

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	80	PIXEL	DECTRIS PILATUS 6M		2016-04-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL12-2	0.97946	SSRL	BL12-2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rrim I (All)	Rpim I (All)	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	2.61	43.84	99.9	0.343	0.105	1	10.82	20.8		23763

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.61	2.73			1.526	0.41

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	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	THROUGHOUT	6EB4	2.61	35	22467	1238	99.85	0.19633	0.19424	0.2	0.23214	0.23	RANDOM	71.207

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]
0.6	0.3		0.6		-1.96

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.303
r_dihedral_angle_4_deg	23.98
r_dihedral_angle_3_deg	18.006
r_long_range_B_refined	7.814
r_long_range_B_other	7.813
r_dihedral_angle_1_deg	7.625
r_scangle_other	5.383
r_mcangle_it	4.868
r_mcangle_other	4.867
r_scbond_it	3.329
r_scbond_other	3.328
r_mcbond_it	2.994
r_mcbond_other	2.994
r_angle_refined_deg	1.83
r_angle_other_deg	1.371
r_chiral_restr	0.075
r_bond_refined_d	0.012
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4100
Nucleic Acid Atoms
Solvent Atoms	19
Heterogen Atoms	40

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing