8JMY

Crystal structure of Rv2186c in Mycobacterium tuberculosis

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, SITTING DROP	7.1	289	0.1M Tris-HCl, pH7.1, 0.3M MgCl2, 10% PEG 8000

Crystal Properties
Matthews coefficient	Solvent content
2.2	44

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 106.477	α = 90
b = 28.254	β = 100.771
c = 86.779	γ = 90

Symmetry
Space Group	C 1 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	80	CCD	MARMOSAIC 225 mm CCD		2021-05-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL18U1	0.97915	SSRF	BL18U1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.56	50	95.9	0.074	0.029	0.98	27.8	6.6		36125

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.56	1.59			0.329	0.138	0.949

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 (All)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.563	27.291	36125	1799	98.519	0.16	0.1578	0.2038	Random selection	22.84

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]
-0.966		-0.564	1.182		-0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.951
r_dihedral_angle_3_deg	13.838
r_dihedral_angle_2_deg	12.723
r_dihedral_angle_1_deg	6.617
r_rigid_bond_restr	4.542
r_lrange_it	3.993
r_lrange_other	3.915
r_scangle_it	3.182
r_scangle_other	3.181
r_mcangle_other	2.682
r_mcangle_it	2.675
r_scbond_it	2.352
r_scbond_other	2.351
r_mcbond_it	2.044
r_mcbond_other	2.039
r_angle_refined_deg	1.633
r_angle_other_deg	0.585
r_symmetry_nbd_refined	0.305
r_nbd_other	0.253
r_nbd_refined	0.223
r_symmetry_nbd_other	0.191
r_nbtor_refined	0.179
r_symmetry_xyhbond_nbd_refined	0.178
r_xyhbond_nbd_refined	0.148
r_ncsr_local_group_1	0.129
r_chiral_restr	0.091
r_symmetry_nbtor_other	0.081
r_bond_refined_d	0.011
r_gen_planes_refined	0.01
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1950
Nucleic Acid Atoms
Solvent Atoms	218
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing