4K73

X-ray crystal structure of an L,D-transpeptidase from Mycobacterium tuberculosis H37Rv

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	289	MCSG1 E9: 0.2 M calcium chloride, 20% PEG3350, pH 7.50, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
1.85	33.64

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 44.24	α = 90
b = 46.44	β = 90
c = 111.17	γ = 90

Symmetry
Space Group	P 21 21 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	CCD	ADSC QUANTUM 315		2013-01-26	M	SINGLE WAVELENGTH
2	1	x-ray	100	CCD	RIGAKU SATURN 944+		2013-04-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.1	0.977408	ALS	5.0.1
2	ROTATING ANODE	RIGAKU FR-E+ SUPERBRIGHT	1.54

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
1,2	1.65	50	99.1	0.052	18.23	4.2	28399	28136

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	SAD	THROUGHOUT	1.65	46.48	28399	26663	1416	99.08	0.19753	0.19571	0.23077	RANDOM	21.014

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]
-0.95			-0.35		1.31

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	25.807
r_dihedral_angle_4_deg	16.744
r_dihedral_angle_3_deg	12.272
r_dihedral_angle_1_deg	6.3
r_angle_refined_deg	1.712
r_mcangle_it	1.547
r_scbond_it	1.094
r_angle_other_deg	0.929
r_mcbond_it	0.922
r_mcbond_other	0.922
r_chiral_restr	0.093
r_bond_refined_d	0.014
r_gen_planes_refined	0.007
r_bond_other_d	0.002
r_gen_planes_other	0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1644
Nucleic Acid Atoms
Solvent Atoms	252
Heterogen Atoms	1

Software

Software
Software Name	Purpose
PHENIX	model building
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
PHENIX	phasing