Experiment: 6TYJ

Crystal structure of zinc-bound Hemerythrin HHE cation binding domain-containing protein (soak): Rv2633c homolog from Mycobacterium kansasii

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6PIE	PDB entry 6pie, apo structure

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		290	Optimization screen around condition MCSG1-H6, well C1: 3.0M sodium formate, 100mM Sodium acetate / HCl pH 4.43: MykaA.20209.a.B11.PB00104 at 22mg/ml, iron-containing red protein: O/N soak with 5mM ZnCl2: cryo: direct: tray 311000c1: puck ydb7-6

Crystal Properties
Matthews coefficient	Solvent content
2.11	41.83

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 52.23	α = 90
b = 52.23	β = 90
c = 104.65	γ = 120

Symmetry
Space Group	P 31 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	CCD	RAYONIX MX-300		2019-07-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-F	0.97872	APS	21-ID-F

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim 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	1.6	50	100	0.05	0.052	0.999	24.28	10.2		22570			22.68

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.6	1.64	100		0.558	0.605	0.918	3.19	6.693

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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	FREE R-VALUE	PDB entry 6pie, apo structure	1.6	45.23	1.37	22495	2012	99.84	0.1802	0.1775	0.1829	0.2076	0.2109	0	32.4

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	16.9394
f_angle_d	0.8953
f_chiral_restr	0.0537
f_bond_d	0.008
f_plane_restr	0.0074

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1268
Nucleic Acid Atoms
Solvent Atoms	153
Heterogen Atoms	4

Software

Software
Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PDB_EXTRACT	data extraction
PHASER	phasing