8Z9B

Low molecular weight antigen MTB12

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293.15	1.8 M Ammonium sulfate, 0.1 M Citric acid pH 3.7

Crystal Properties
Matthews coefficient	Solvent content
4.5	72.69

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 100.67	α = 90
b = 100.67	β = 90
c = 98.53	γ = 90

Symmetry
Space Group	P 41 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	125	PIXEL	STFC Large Pixel Detector		2023-12-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PAL/PLS BEAMLINE 5C (4A)	0.97942	PAL/PLS	5C (4A)

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	2.68	29.84	99.82	0.999	22.6	26.1		14762

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.68	2.776			0.768

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	AlphaFold	2.68	29.84	14755	739	99.831	0.279	0.2777	0.304	94.44

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]
-3.579			-3.579		7.158

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.219
r_dihedral_angle_4_deg	18.721
r_dihedral_angle_3_deg	17.628
r_lrange_it	12.672
r_lrange_other	12.669
r_scangle_it	10.716
r_scangle_other	10.704
r_mcangle_it	9.832
r_mcangle_other	9.828
r_scbond_it	7.276
r_scbond_other	7.273
r_mcbond_other	6.463
r_mcbond_it	6.462
r_dihedral_angle_1_deg	6.045
r_angle_other_deg	2.395
r_angle_refined_deg	1.813
r_nbd_other	0.33
r_symmetry_nbd_other	0.254
r_nbd_refined	0.233
r_xyhbond_nbd_refined	0.192
r_nbtor_refined	0.183
r_symmetry_xyhbond_nbd_refined	0.181
r_symmetry_nbd_refined	0.154
r_symmetry_xyhbond_nbd_other	0.104
r_chiral_restr	0.094
r_symmetry_nbtor_other	0.081
r_bond_other_d	0.037
r_bond_refined_d	0.016
r_gen_planes_refined	0.005
r_gen_planes_other	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1620
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
PHENIX	phasing