7PFN | pdb_00007pfn

Acetyllysine73-incorporated OXA-48 complexed with imipenem in both active and inactive acyl-enzyme intermediates

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	7.5	291	0.1M HEPES pH 7.5, 11.6% PEG8000, 8% 1-BuOH, mixed with the 10 mg/mL protein stock at 1:1 ratio.

Crystal Properties
Matthews coefficient	Solvent content
2.42	49.27

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 44.799	α = 90
b = 104.995	β = 90
c = 124.745	γ = 90

Symmetry
Space Group	P 2 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		2021-07-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.976292	Diamond	I03

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	1.8	62.37	100	0.997	9.9	11.4		55552

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	1.8	1.84			0.588	1.1

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	1.8	62.37	55487	2745	99.993	0.18	0.1778	0.1786	0.2137	0.2153	25.438

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]
1.471			0.782		-2.252

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.529
r_dihedral_angle_4_deg	19.264
r_dihedral_angle_3_deg	13.434
r_dihedral_angle_1_deg	6.301
r_lrange_it	5.75
r_lrange_other	5.693
r_scangle_it	4.728
r_scangle_other	4.717
r_scbond_it	3.069
r_scbond_other	3.063
r_mcangle_it	2.87
r_mcangle_other	2.87
r_mcbond_it	2.022
r_mcbond_other	2.018
r_angle_refined_deg	1.539
r_angle_other_deg	1.395
r_nbd_refined	0.213
r_symmetry_nbd_other	0.171
r_nbtor_refined	0.171
r_nbd_other	0.164
r_xyhbond_nbd_refined	0.14
r_symmetry_xyhbond_nbd_other	0.122
r_symmetry_nbd_refined	0.119
r_ncsr_local_group_1	0.106
r_symmetry_xyhbond_nbd_refined	0.096
r_chiral_restr	0.08
r_symmetry_nbtor_other	0.077
r_bond_refined_d	0.01
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3975
Nucleic Acid Atoms
Solvent Atoms	365
Heterogen Atoms	70

Software

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