7O9N

Crystal Structure of a Class D Carbapenemase Complexed with Bicarbonate

X-RAY DIFFRACTION

---

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
2.24	45.15

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 81.807	α = 90
b = 106.404	β = 90
c = 124.706	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 EIGER2 XE 16M		2020-12-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.976254	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	1.97	81.81	100	0.995	6	13.2		77632

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	1.97	2.01			0.582	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	1.97	68.496	77539	3748	99.981	0.2	0.1954	0.2861	25.536

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]
-1.123			-0.957		2.08

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.024
r_dihedral_angle_4_deg	18.049
r_dihedral_angle_3_deg	13.572
r_rigid_bond_restr	9.944
r_lrange_it	6.67
r_lrange_other	6.582
r_dihedral_angle_1_deg	6.494
r_scangle_it	5.806
r_scangle_other	5.793
r_mcangle_it	5.295
r_mcangle_other	5.294
r_scbond_it	4.803
r_scbond_other	4.798
r_mcbond_it	4.215
r_mcbond_other	4.209
r_angle_refined_deg	1.466
r_angle_other_deg	1.327
r_symmetry_nbd_refined	0.314
r_nbd_other	0.249
r_nbd_refined	0.217
r_xyhbond_nbd_refined	0.184
r_symmetry_nbd_other	0.182
r_nbtor_refined	0.166
r_symmetry_xyhbond_nbd_refined	0.148
r_symmetry_nbtor_other	0.075
r_ncsr_local_group_2	0.072
r_ncsr_local_group_4	0.072
r_chiral_restr	0.07
r_ncsr_local_group_3	0.066
r_ncsr_local_group_5	0.064
r_ncsr_local_group_6	0.057
r_symmetry_xyhbond_nbd_other	0.055
r_ncsr_local_group_1	0.045
r_bond_refined_d	0.009
r_gen_planes_refined	0.007
r_bond_other_d	0.004
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8029
Nucleic Acid Atoms
Solvent Atoms	614
Heterogen Atoms	20

Software

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