8IX8

Crystal structure of Class A beta-lactamase BlaA WT - complex with Tebipenem

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5E2E

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	293	0.1 M TRIS hydrochloride pH 8.5, 2.0 M Ammonium phosphate monobasic

Crystal Properties
Matthews coefficient	Solvent content
2.25	45.39

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 91.342	α = 90
b = 72.182	β = 96.087
c = 43.543	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	PIXEL	RIGAKU HyPix-6000HE	X ray optics	2022-11-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.54

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	1.5	27.92	99.9	0.104	0.111	0.038	0.998	14	13.7		44966

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	1.5	1.53			1.003	1.13	0.512	0.657		9.2

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 (All)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.5	24.597	44951	2244	99.896	0.169	0.1673	0.2013	14.192

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]
1.177		0.065	-0.555		-0.622

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	19.245
r_dihedral_angle_6_deg	16.073
r_dihedral_angle_3_deg	13.898
r_lrange_it	6.881
r_lrange_other	6.559
r_dihedral_angle_1_deg	6.34
r_scangle_it	4.845
r_scangle_other	4.651
r_scbond_it	3.207
r_scbond_other	3.029
r_mcangle_it	2.168
r_mcangle_other	2.167
r_angle_refined_deg	1.902
r_mcbond_it	1.463
r_mcbond_other	1.459
r_angle_other_deg	0.6
r_symmetry_nbd_refined	0.388
r_nbd_other	0.259
r_nbd_refined	0.229
r_xyhbond_nbd_refined	0.215
r_symmetry_xyhbond_nbd_refined	0.203
r_symmetry_nbd_other	0.186
r_nbtor_refined	0.186
r_chiral_restr	0.093
r_symmetry_nbtor_other	0.088
r_bond_refined_d	0.01
r_gen_planes_refined	0.01
r_symmetry_xyhbond_nbd_other	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	2017
Nucleic Acid Atoms
Solvent Atoms	279
Heterogen Atoms	40

Software

Software
Software Name	Purpose
REFMAC	refinement
Coot	model building
Aimless	data scaling
CrysalisPro	data collection
MOLREP	phasing