8IXX

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

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
2.29	46.42

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 91.743	α = 90
b = 72.818	β = 95.776
c = 43.7	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	2022-08-17	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	1.7	24.663	99.8	0.129	0.152	0.078	0.989	7.4	6.5		31443

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	1.7	1.73			0.523	0.674	0.418	0.809		4

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	1.7	24.663	31440	1608	99.791	0.187	0.185	0.2185	18.766

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]
2.038		0.47	-1.071		-1.04

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	17.411
r_dihedral_angle_6_deg	15.575
r_dihedral_angle_3_deg	13.595
r_dihedral_angle_1_deg	6.731
r_lrange_it	6.315
r_lrange_other	5.81
r_scangle_it	4.247
r_scangle_other	4.14
r_scbond_it	2.807
r_scbond_other	2.709
r_mcangle_it	2.363
r_mcangle_other	2.361
r_mcbond_it	1.669
r_mcbond_other	1.668
r_angle_refined_deg	1.638
r_angle_other_deg	0.533
r_xyhbond_nbd_refined	0.226
r_nbd_refined	0.22
r_symmetry_nbd_other	0.191
r_symmetry_xyhbond_nbd_refined	0.183
r_nbtor_refined	0.181
r_symmetry_nbd_refined	0.171
r_nbd_other	0.17
r_chiral_restr	0.082
r_symmetry_nbtor_other	0.082
r_chiral_restr_other	0.02
r_gen_planes_refined	0.009
r_bond_refined_d	0.008
r_symmetry_xyhbond_nbd_other	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2004
Nucleic Acid Atoms
Solvent Atoms	216
Heterogen Atoms	48

Software

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