6U3L | pdb_00006u3l

Crystal structure of Hemerythrin HHE cation binding domain-containing protein: Rv2633c homolog from Mycobacterium kansasii

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		290	MCSG-1 screen F3: 200mM ammonium citrate, 25% PEG 3350: MykaA.20209.a.B11.PB00101 at 2mg/ml, grown at 14C: cryo: 20% EG: tray 308332F3: puck vlf8-4. For experimental phasing, a crystal from MCSG-1 screen, condition F3 (200mM ammonium citrate, 25% PEG 3350) with MykaA.20209.a B1.PB00101 at 3mg/ml, grown at 14C, was incubated for 15 sec each in a solution of 90% reservoir and 10% 2.5M sodium iodide in ethylene glycol, and then in a solution of 80% reservoir and 20% 2.5M sodium iodide in ethylene glycol, and vitrified in liquid nitrogen: tray 308326f3: puck fdn8-5

Crystal Properties
Matthews coefficient	Solvent content
2.1	41.45

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 52.05	α = 90
b = 52.05	β = 90
c = 104.7	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		2010-03-21	M	SINGLE WAVELENGTH
2	1	x-ray	100	CCD	RIGAKU SATURN 944+		2010-03-18	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
2	ROTATING ANODE	RIGAKU FR-E+ SUPERBRIGHT	1.5418

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	1.75	50	100	0.041	0.044	1	24.94	6.91		17189			28.21

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	1.75	1.8	99.9		0.639	0.716	0.85	2.18	4.944

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	SAD	FREE R-VALUE	1.75	45.08	1.35	17176	1695	99.89	0.1819	0.178	0.18	0.2179	0.22	0	36.05

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	13.9897
f_angle_d	0.8509
f_chiral_restr	0.0483
f_bond_d	0.0079
f_plane_restr	0.0065

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1266
Nucleic Acid Atoms
Solvent Atoms	118
Heterogen Atoms	4

Software

Software
Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
PHASER	phasing
PARROT	phasing
ARP/wARP	model building
Coot	model building

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.