7PGO

Crystal Structure of a Class D Carbapenemase_R250A

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
2.36	47.92

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 84.546	α = 90
b = 108.2	β = 90
c = 124.61	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	PIXEL	DECTRIS EIGER X 16M		2021-05-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.918395	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	1.85	58.75	100	0.996	6.6	23.2		98044

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	1.85	1.88			0.737	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	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	4S2P	1.85	58.75	97955	5022	99.914	0.207	0.2052	0.234	20.915

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]
2.548			-0.76		-1.788

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.622
r_dihedral_angle_4_deg	15.909
r_dihedral_angle_3_deg	13.713
r_dihedral_angle_1_deg	6.027
r_lrange_it	5.395
r_lrange_other	5.313
r_scangle_it	3.453
r_scangle_other	3.452
r_mcangle_it	2.943
r_mcangle_other	2.943
r_scbond_it	2.149
r_scbond_other	2.149
r_mcbond_it	1.824
r_mcbond_other	1.824
r_angle_refined_deg	1.435
r_angle_other_deg	1.366
r_symmetry_nbd_refined	0.267
r_nbd_other	0.22
r_nbd_refined	0.218
r_symmetry_nbd_other	0.171
r_nbtor_refined	0.168
r_xyhbond_nbd_refined	0.166
r_symmetry_xyhbond_nbd_refined	0.151
r_symmetry_nbtor_other	0.076
r_ncsr_local_group_5	0.074
r_chiral_restr	0.073
r_ncsr_local_group_3	0.071
r_ncsr_local_group_2	0.07
r_ncsr_local_group_4	0.07
r_ncsr_local_group_6	0.057
r_ncsr_local_group_1	0.051
r_bond_refined_d	0.009
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7956
Nucleic Acid Atoms
Solvent Atoms	901
Heterogen Atoms	25

Software

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