8SQG | pdb_00008sqg

OXA-48 bound to inhibitor CDD-2801

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6P96

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	298	25% (v/v) PEG 550 MME, 0.1 M TRIS-HCl pH 8.5

Crystal Properties
Matthews coefficient	Solvent content
3.06	59.87

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 121.929	α = 90
b = 121.929	β = 90
c = 160.522	γ = 120

Symmetry
Space Group	P 65 2 2

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 PILATUS3 S 2M		2022-12-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.2.2	1.00002	ALS	8.2.2

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	2.03	33.52	99.88	0.999	20.08	22.7		46045			27.02

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	2.03	2.103			0.914	3.35

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.03	33.52	1.34	46010	2426	99.92	0.1935	0.1914	0.1953	0.2267	0.2276	30.73

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]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	14.8696
f_angle_d	0.8551
f_chiral_restr	0.0554
f_bond_d	0.0076
f_plane_restr	0.0061

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3927
Nucleic Acid Atoms
Solvent Atoms	263
Heterogen Atoms	72

Software

Software
Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing