7ZM4

Crystal structure of HsaD from Mycobacterium tuberculosis in complex with Cyclipostin-like inhibitor CyC31

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7ZJT

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	293	MES Na 0.1 M NH4SO4 1.55 M PEG400 6.88%

Crystal Properties
Matthews coefficient	Solvent content
2.68	54.11

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 76.684	α = 90
b = 87.224	β = 90
c = 105.725	γ = 90

Symmetry
Space Group	P 2 2 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	PIXEL	DECTRIS EIGER X 16M		2021-11-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SOLEIL BEAMLINE PROXIMA 1	0.978565	SOLEIL	PROXIMA 1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	1.62	45.21	99.7	0.081	0.084	0.023	0.999	17.2	13.5		91211			19.648

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	1.62	1.64	94.7		1.466	1.528	0.424	0.738		12.3

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	7ZJT	1.62	45.21	86530	4646	99.76	0.1846	0.1836	0.2022	RANDOM	24.242

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]
0.11			0.56		-0.66

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.115
r_dihedral_angle_4_deg	17.621
r_dihedral_angle_3_deg	12.197
r_dihedral_angle_1_deg	6.835
r_angle_refined_deg	1.368
r_angle_other_deg	1.356
r_chiral_restr	0.07
r_bond_refined_d	0.007
r_gen_planes_refined	0.006
r_bond_other_d	0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.115
r_dihedral_angle_4_deg	17.621
r_dihedral_angle_3_deg	12.197
r_dihedral_angle_1_deg	6.835
r_angle_refined_deg	1.368
r_angle_other_deg	1.356
r_chiral_restr	0.07
r_bond_refined_d	0.007
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4388
Nucleic Acid Atoms
Solvent Atoms	377
Heterogen Atoms	35

Software

Software
Software Name	Purpose
Aimless	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	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.