7O5N | pdb_00007o5n

OXA-48 with decarbamylated Lys73 in complex with avibactam at pH 8.0

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4S2P

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	291	0.1M HEPES,pH=8.0, 10%PEG 8000, 4% 1-butanol, 10mM Avibactam, mixed with the 10 mg/mL protein stock at 1:1 ratio.

Crystal Properties
Matthews coefficient	Solvent content
2.52	51.17

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 89.749	α = 90
b = 107.959	β = 90
c = 125.675	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	CCD	ADSC QUANTUM 315r		2019-04-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL17U1	0.979191	SSRF	BL17U1

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	1.6	81.89	99.9	0.999	12.1	13.2		160843

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	1.6	1.63			0.747	1.2

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	4S2P	1.6	73.144	160736	7894	99.847	0.189	0.188	0.1849	0.2157	0.2131	33.332

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]
4.545			-1.869		-2.676

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.59
r_dihedral_angle_4_deg	17.482
r_dihedral_angle_3_deg	12.999
r_lrange_it	6.297
r_lrange_other	6.241
r_dihedral_angle_1_deg	6.131
r_scangle_it	5.336
r_scangle_other	5.336
r_scbond_it	3.605
r_scbond_other	3.598
r_mcangle_it	3.196
r_mcangle_other	3.185
r_mcbond_it	2.411
r_mcbond_other	2.4
r_angle_refined_deg	1.589
r_angle_other_deg	1.438
r_chiral_restr_other	0.226
r_nbd_refined	0.216
r_nbd_other	0.19
r_symmetry_nbd_other	0.174
r_nbtor_refined	0.172
r_symmetry_nbd_refined	0.172
r_xyhbond_nbd_refined	0.157
r_symmetry_xyhbond_nbd_refined	0.149
r_symmetry_nbtor_other	0.08
r_chiral_restr	0.079
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	7929
Nucleic Acid Atoms
Solvent Atoms	692
Heterogen Atoms	119

Software

Software
Software Name	Purpose
REFMAC	refinement
xia2	data reduction
Aimless	data scaling
MOLREP	phasing