9XFW | pdb_00009xfw

Crystal structure of Class A beta-lactamase BlaA in complex with Meropenem (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	46.37

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 91.774	α = 90
b = 72.619	β = 94.953
c = 43.707	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		2022-10-05	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	2	24.53	99.9	0.199	0.199	0.091	0.991	8.2	10.9		19371

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2	2.05			0.889

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	2	24.53	19370	940	99.871	0.21	0.2067	0.2084	0.2706	0.2727	22.059

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]
2.467		0.961	-1.27		-1.344

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	14.013
r_dihedral_angle_3_deg	12.694
r_dihedral_angle_2_deg	8.929
r_lrange_it	7.294
r_dihedral_angle_1_deg	6.642
r_scangle_it	3.871
r_scbond_it	2.53
r_mcangle_it	2.511
r_angle_refined_deg	1.805
r_mcbond_it	1.65

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	14.013
r_dihedral_angle_3_deg	12.694
r_dihedral_angle_2_deg	8.929
r_lrange_it	7.294
r_dihedral_angle_1_deg	6.642
r_scangle_it	3.871
r_scbond_it	2.53
r_mcangle_it	2.511
r_angle_refined_deg	1.805
r_mcbond_it	1.65
r_nbtor_refined	0.308
r_symmetry_xyhbond_nbd_refined	0.242
r_nbd_refined	0.23
r_xyhbond_nbd_refined	0.196
r_symmetry_nbd_refined	0.168
r_chiral_restr	0.139
r_bond_refined_d	0.007
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1992
Nucleic Acid Atoms
Solvent Atoms	176
Heterogen Atoms	31

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.