9XFY | pdb_00009xfy

Crystal structure of Class A beta-lactamase BlaA in complex with ertapenem (imine form)

X-RAY DIFFRACTION

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	45.85

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		2022-08-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.54184

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	0.142	0.154	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			0.591	0.682	0.332	0.809

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	5E2E	1.7	24.663	31442	1608	99.791	0.196	0.1936	0.195	0.2298	0.2307	21.318

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]
2.066		0.45	-1.124		-1.012

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	13.008
r_dihedral_angle_3_deg	11.961
r_dihedral_angle_2_deg	10.633
r_lrange_it	8.981
r_dihedral_angle_1_deg	6.668
r_scangle_it	4.741
r_scbond_it	3.131
r_mcangle_it	2.396
r_angle_refined_deg	2.046
r_mcbond_it	1.711

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	13.008
r_dihedral_angle_3_deg	11.961
r_dihedral_angle_2_deg	10.633
r_lrange_it	8.981
r_dihedral_angle_1_deg	6.668
r_scangle_it	4.741
r_scbond_it	3.131
r_mcangle_it	2.396
r_angle_refined_deg	2.046
r_mcbond_it	1.711
r_nbtor_refined	0.31
r_nbd_refined	0.227
r_symmetry_nbd_refined	0.208
r_chiral_restr	0.171
r_xyhbond_nbd_refined	0.171
r_symmetry_xyhbond_nbd_refined	0.138
r_bond_refined_d	0.01
r_gen_planes_refined	0.01

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2004
Nucleic Acid Atoms
Solvent Atoms	212
Heterogen Atoms	48

Software

Software
Software Name	Purpose
REFMAC	refinement
CrysalisPro	data reduction
CrysalisPro	data scaling
MOLREP	phasing

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.