9V49 | pdb_00009v49

Crystal Structure of 2R, 3S-Xeruborbactam with SME-1

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1DY6

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	0.2M lithium chloride, 20%PEG 4000

Crystal Properties
Matthews coefficient	Solvent content
2.05	40.13

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 70.98	α = 90
b = 51.237	β = 113.404
c = 74.856	γ = 90

Symmetry
Space Group	P 1 21 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		2024-09-10	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)	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	2.2	23.683	99.9	0.996	11.2	7.4		25335

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	2.27			0.753

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.2	23.683	25322	1261	99.89	0.19	0.187	0.1877	0.2492	0.2505	20.912

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]
-0.55		-0.425	-0.62		1.119

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	27.305
r_dihedral_angle_3_deg	17.211
r_dihedral_angle_6_deg	14.802
r_dihedral_angle_1_deg	7.332
r_lrange_it	6.464
r_scangle_it	4.622
r_scbond_it	3
r_mcangle_it	2.889
r_angle_refined_deg	2.155
r_mcbond_it	1.859
r_nbtor_refined	0.31
r_symmetry_nbd_refined	0.275
r_metal_ion_refined	0.248
r_nbd_refined	0.232
r_xyhbond_nbd_refined	0.205
r_symmetry_xyhbond_nbd_refined	0.194
r_chiral_restr	0.149
r_bond_refined_d	0.009
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4116
Nucleic Acid Atoms
Solvent Atoms	104
Heterogen Atoms	72

Software

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