Experiment: 7F8P

Crystal structure of the Mycobacterium tuberculosis L,D-transpeptidase-2 (LdtMt2) with new carbapenem drug T203

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5DU7

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		298	20% 5000 MME, 200mM Ammonium sulfate

Crystal Properties
Matthews coefficient	Solvent content
2.88	57.36

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 60.799	α = 90
b = 94.278	β = 93.136
c = 75.707	γ = 90

Symmetry
Space Group	P 1 21 1

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	ADSC QUANTUM 315		2016-04-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	1.0	APS	19-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	1.7	30.35	97.4	0.073	0.062	0.082	0.036	0.97	23.7	5		2095305			11.97

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.7	1.73	95.9		0.738	0.845	0.823	0.364	0.852	3.4	5

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	5DU7	1.7	30.35	1.35	147316	3275	80.29	0.1659	0.1654	0.1647	0.1876	0.188	16.58

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]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	20.6799
f_angle_d	0.9687
f_chiral_restr	0.0598
f_bond_d	0.0064
f_plane_restr	0.0051

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5274
Nucleic Acid Atoms
Solvent Atoms	854
Heterogen Atoms	71

Software

Software
Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling