4OQ0 | pdb_00004oq0

Crystal structure of stabilized TEM-1 beta-lactamase variant v.13 carrying R164S/G238S mutation in complex with boron-based inhibitor EC25

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		6.2	293	9% (wt/vol) polyethylene glycol (PEG) 8000, 100 mM MES, and 200mM Ca(OAc)2, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.11	41.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 152.76	α = 90
b = 46.18	β = 92.72
c = 34.47	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	IMAGE PLATE	RIGAKU RAXIS IV++			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RUH3R

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym I (Observed)	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	1.42	26.2		0.038	27.63			42706		3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.42	1.6	89.5		0.14	10.86	5.62

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.42	26.2	40569	2136	93.9	0.1	0.098	0.1194	0.138	0.157	RANDOM	16.23

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]
-0.1		0.11	0.15		-0.05

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.357
r_sphericity_free	24.078
r_dihedral_angle_4_deg	21.586
r_dihedral_angle_3_deg	14.426
r_sphericity_bonded	11.534
r_dihedral_angle_1_deg	7.237
r_rigid_bond_restr	6.531
r_long_range_B_refined	5.787
r_long_range_B_other	5.586
r_scangle_other	5.092
r_scbond_it	4.62
r_scbond_other	4.605
r_mcangle_it	3.77
r_mcangle_other	3.768
r_mcbond_other	3.497
r_mcbond_it	3.496
r_angle_refined_deg	2.044
r_angle_other_deg	1.039
r_chiral_restr	0.136
r_bond_refined_d	0.021
r_gen_planes_refined	0.012
r_gen_planes_other	0.003
r_bond_other_d	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2012
Nucleic Acid Atoms
Solvent Atoms	283
Heterogen Atoms	37

Software

Software
Software Name	Purpose
StructureStudio	data collection
MOLREP	phasing
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling