4KK7 | pdb_00004kk7

Structure of EccB1 from the type VII (ESX-1) secretion system of Mycobacterium tuberculosis.

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.4	295	0.1M TRIS-HCL PH 5.6, 15% PEG2000 MME, 0.01M NI CHLORIDE, vapor diffusion, sitting drop, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.32	46.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 31.7	α = 90
b = 110.63	β = 90
c = 110.51	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	MARMOSAIC 300 mm CCD		2012-04-15	M	SINGLE WAVELENGTH
2	1	x-ray	100	CCD	MARMOSAIC 300 mm CCD		2012-04-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID	1.0	APS	22-ID
2	SYNCHROTRON	APS BEAMLINE 22-ID	1.5	APS	22-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.68	50	94.1	0.053	14.2			42744		-3	33.825

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1,2	1.68	1.72	85.4		0.99	1.16

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	SAD	THROUGHOUT	1.68	49.48	40651	2118	94.18	0.1786	0.1768	0.1868	0.214	0.2202	RANDOM	30.0072

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]
0.3			0.14		-0.43

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.893
r_dihedral_angle_4_deg	16.114
r_dihedral_angle_3_deg	11.674
r_dihedral_angle_1_deg	5.46
r_mcangle_it	1.678
r_angle_refined_deg	1.347
r_mcbond_it	1.035
r_mcbond_other	1.035
r_angle_other_deg	0.758
r_chiral_restr	0.075

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.893
r_dihedral_angle_4_deg	16.114
r_dihedral_angle_3_deg	11.674
r_dihedral_angle_1_deg	5.46
r_mcangle_it	1.678
r_angle_refined_deg	1.347
r_mcbond_it	1.035
r_mcbond_other	1.035
r_angle_other_deg	0.758
r_chiral_restr	0.075
r_bond_refined_d	0.009
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2870
Nucleic Acid Atoms
Solvent Atoms	347
Heterogen Atoms	18

Software

Software
Software Name	Purpose
XSCALE	data scaling
SHARP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
SERGUI	data collection
XDS	data reduction

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.