7ZM3 | pdb_00007zm3

Crystal structure of HsaD from Mycobacterium tuberculosis in complex with Cyclipostin-like inhibitor CyC17

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 1.656 M PEG400 6.88%

Crystal Properties
Matthews coefficient	Solvent content
2.7	54.54

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 76.958	α = 90
b = 87.404	β = 90
c = 106.128	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 9M		2021-07-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SOLEIL BEAMLINE PROXIMA 2	0.980114	SOLEIL	PROXIMA 2

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	1.81	45.36	99.8	0.118	0.122	0.033	0.999	16.5	13.4		66020			19.116

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	1.81	1.85	96		1.39	1.449	0.404	0.638		12.4

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	7ZJT	1.81	45.36	62617	3372	99.74	0.1839	0.1823	0.19	0.2132	0.22	RANDOM	26.724

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]
-0.5			0.92		-0.42

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.46
r_dihedral_angle_4_deg	16.217
r_dihedral_angle_3_deg	12.625
r_dihedral_angle_1_deg	6.736
r_angle_refined_deg	1.517
r_angle_other_deg	1.363
r_chiral_restr	0.076
r_bond_refined_d	0.009
r_gen_planes_refined	0.007
r_bond_other_d	0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.46
r_dihedral_angle_4_deg	16.217
r_dihedral_angle_3_deg	12.625
r_dihedral_angle_1_deg	6.736
r_angle_refined_deg	1.517
r_angle_other_deg	1.363
r_chiral_restr	0.076
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	4388
Nucleic Acid Atoms
Solvent Atoms	336
Heterogen Atoms	20

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.