3ONR | pdb_00003onr

Crystal structure of the calcium chelating immunodominant antigen, calcium dodecin (Rv0379),from Mycobacterium tuberculosis with a novel calcium-binding site

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	vapor diffusion,hanging and sitting drops	8	291	1M Sodium Formate, 10mM CaCl2, pH 8.0, vapor diffusion,hanging and sitting drops, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.17	43.41

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 70.193	α = 90
b = 78.446	β = 90
c = 152.489	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				M	MAD
2	1	x-ray		M	SINGLE WAVELENGTH
3	1
4	1

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 14-BM-D	1.071, 1.072, 1.100	APS	14-BM-D
2	SYNCHROTRON	APS BEAMLINE 14-BM-C		APS	14-BM-C
3	SYNCHROTRON	APS BEAMLINE 19-ID		APS	19-ID
4	SYNCHROTRON	APS BEAMLINE 23-ID-B		APS	23-ID-B

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	1.8	76.7		0.027	20.8	1.9		78271

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	MAD	THROUGHOUT	1.8	28.88	78271	3927	99.08	0.1835	0.1812	0.2	0.2293	0.25	RANDOM	30.704

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]
0.47			-0.93		0.46

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.553
r_dihedral_angle_4_deg	17.195
r_dihedral_angle_3_deg	16.172
r_scangle_it	6.599
r_dihedral_angle_1_deg	6.399
r_scbond_it	4.061
r_mcangle_it	2.212
r_angle_refined_deg	2.062
r_mcbond_it	1.306
r_chiral_restr	0.169

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.553
r_dihedral_angle_4_deg	17.195
r_dihedral_angle_3_deg	16.172
r_scangle_it	6.599
r_dihedral_angle_1_deg	6.399
r_scbond_it	4.061
r_mcangle_it	2.212
r_angle_refined_deg	2.062
r_mcbond_it	1.306
r_chiral_restr	0.169
r_bond_refined_d	0.025
r_gen_planes_refined	0.01

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6402
Nucleic Acid Atoms
Solvent Atoms	424
Heterogen Atoms	43

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling
SHARP	phasing

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.