8SDR

Crystal structure of PDC-3 beta-lactamase in complex with the boronic acid inhibitor LP-06

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3S22

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		273	100 mM Imidazole pH 7.0, 2-8% isopropyl alcohol (IPA), and 16-34% PEG 3350. Protein was in 10 mM HEPES pH 7.5, 150 mM NaCl and 5% glycerol

Crystal Properties
Matthews coefficient	Solvent content
1.97	37.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 44.828	α = 90
b = 71.667	β = 90
c = 106.729	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	100	PIXEL	DECTRIS EIGER X 16M		2019-12-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS-II BEAMLINE 17-ID-2	0.97933	NSLS-II	17-ID-2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.35	28	99.7	0.134	0.998	14.8	12.8		76325

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.35	1.38	96.1		0.626	0.896	3

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.35	28	72326	3919	99.69	0.1309	0.1292	0.1615	RANDOM	11.046

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]
-0.11			0.02		0.09

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.605
r_dihedral_angle_4_deg	15.149
r_dihedral_angle_3_deg	12.894
r_dihedral_angle_1_deg	6.408
r_angle_refined_deg	1.605
r_angle_other_deg	1.493
r_rigid_bond_restr	1.285
r_chiral_restr	0.087
r_bond_refined_d	0.01
r_gen_planes_refined	0.009

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.605
r_dihedral_angle_4_deg	15.149
r_dihedral_angle_3_deg	12.894
r_dihedral_angle_1_deg	6.408
r_angle_refined_deg	1.605
r_angle_other_deg	1.493
r_rigid_bond_restr	1.285
r_chiral_restr	0.087
r_bond_refined_d	0.01
r_gen_planes_refined	0.009
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2781
Nucleic Acid Atoms
Solvent Atoms	593
Heterogen Atoms	27

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
XDS	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.