4HU2 | pdb_00004hu2

Crystal structure of LdtMt2, a L,D-transpeptidase from Mycobacterium tuberculosis: domain A and B

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	293	25% (w/v) PEG 3350, 0.2 M (NH4)2SO4, 0.1 M Bis-TRIS propane, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.24	45.15

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 114.433	α = 90
b = 27.638	β = 114.14
c = 67.99	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	100	CCD	ADSC QUANTUM 210		2012-01-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-1	0.9334	ESRF	ID14-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.46	33.7	98.9	0.038			34254	34254	2.8	2.8

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.456	1.493	98.9		0.489	0.489	2.8	2	34254

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	Cut-off Sigma (F)	Number Reflections (All)	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	1.46	33.7	2.8	2.8	32519	32519	1728	98.85	0.16525	0.16239	0.17	0.21813	0.22	RANDOM	16.55

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]
0.02		-0.22	0.28		-0.47

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.598
r_sphericity_free	31.242
r_dihedral_angle_4_deg	16.443
r_dihedral_angle_3_deg	11.252
r_sphericity_bonded	10.183
r_dihedral_angle_1_deg	5.659
r_rigid_bond_restr	3.062
r_angle_refined_deg	1.44
r_angle_other_deg	0.928
r_chiral_restr	0.082

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.598
r_sphericity_free	31.242
r_dihedral_angle_4_deg	16.443
r_dihedral_angle_3_deg	11.252
r_sphericity_bonded	10.183
r_dihedral_angle_1_deg	5.659
r_rigid_bond_restr	3.062
r_angle_refined_deg	1.44
r_angle_other_deg	0.928
r_chiral_restr	0.082
r_bond_refined_d	0.009
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	1455
Nucleic Acid Atoms
Solvent Atoms	309
Heterogen Atoms	10

Software

Software
Software Name	Purpose
DNA	data collection
PHASER	phasing
REFMAC	refinement
XDS	data reduction
SCALA	data scaling

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.