Experiment: 9JV8

Crystal structure of M. tuberculosis EccCb1-D2 domain

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4N1A	CYTOPLASMIC DOMAIN OF THE THERMOMONOSPORA CURVATA TYPE VII SECRETION ATPASE ECCC

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.6	277	0.1M Sodium citrate tribasic dihydrate pH 5.6, 20% (v/v) PEG 4000 and 20% (v/v) 2-Propanol

Crystal Properties
Matthews coefficient	Solvent content
2.21	43.86

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 37.389	α = 90
b = 75.642	β = 90
c = 102.524	γ = 90

Symmetry
Space Group	P 21 21 21

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	MAR CCD 165 mm		2020-05-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	BRUKER TURBO X-RAY SOURCE	1.5418

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)	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	2.2	35	99.5	0.089	0.02	0.092	0.025	0.99	14.5	13.9		15346			22

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.2	2.28	95.6		0.245	0.255	0.07	0.986		13.2

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	MOLECULAR REPLACEMENT	THROUGHOUT	2.2	28.05	1.34	15284	1528	99.45	0.1819	0.1767	0.1816	0.2285	0.229	0.10	31

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	10.439
f_angle_d	1.009
f_chiral_restr	0.061
f_bond_d	0.007
f_plane_restr	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2160
Nucleic Acid Atoms
Solvent Atoms	154
Heterogen Atoms	32

Software

Software
Software Name	Purpose
PHENIX	refinement
SCALEPACK	data scaling
PHASER	phasing
HKL-3000	data reduction