8DC1 | pdb_00008dc1

Structural and biochemical characterization of L. interrogans Lsa45 reveals a penicillin-binding protein with esterase activity

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	291.15	Solution consisting of 100 mM Tris-HCl, pH 8.5, 30% PEG 1500 and 8% MPD

Crystal Properties
Matthews coefficient	Solvent content
2.42	49.11

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 44.141	α = 90
b = 74.862	β = 90
c = 113.47	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	80	PIXEL	DECTRIS PILATUS 2M		2018-03-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	LNLS BEAMLINE W01B-MX2	1.5499	LNLS	W01B-MX2

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	45.22	99.7	0.171	0.184	0.033	0.999	21.9	31.5		48588			17.64

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	1.65	94.7		2.786	2.858	0.619	0.524	2.1	20.9

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	SAD	THROUGHOUT	1.62	41.17	46108	2405	99.72	0.186	0.18474	0.19	0.21059	0.22	RANDOM	23.489

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]
-1.05			0.04		1.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.966
r_dihedral_angle_4_deg	12.808
r_dihedral_angle_3_deg	11.407
r_long_range_B_refined	8.597
r_long_range_B_other	8.582
r_scangle_other	7.763
r_scbond_it	6.653
r_scbond_other	6.652
r_dihedral_angle_1_deg	5.647
r_mcangle_it	3.396
r_mcangle_other	3.395
r_mcbond_it	2.786
r_mcbond_other	2.786
r_angle_refined_deg	1.336
r_angle_other_deg	1.109
r_chiral_restr	0.088
r_bond_refined_d	0.008
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2734
Nucleic Acid Atoms
Solvent Atoms	216
Heterogen Atoms	30

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
AutoSol	phasing