7PSF | pdb_00007psf

Crystal Structure of a Class D Carbapenemase Complexed with Imipenem

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	HEPES pH 7.5 no Cl-, 11.6% PEG8000, 8% 1-BuOH mixed with the 10 mg/mL protein stock at 1:1 ratio.

Crystal Properties
Matthews coefficient	Solvent content
2.31	46.76

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 83.42	α = 90
b = 107.6	β = 90
c = 124.59	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 X 16M		2020-12-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.918380	Diamond	I04

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	2.1	49.39	99.9	0.998	8.2	13.6		66086

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	2.1	2.15			0.695	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	2.1	49.39	66012	3258	99.853	0.243	0.2408	0.24	0.2778	0.28	36.852

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]
4.549			-0.138		-4.41

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.89
r_dihedral_angle_4_deg	16.666
r_dihedral_angle_3_deg	14.607
r_dihedral_angle_1_deg	6.624
r_lrange_it	6.44
r_lrange_other	6.433
r_scangle_it	5.007
r_scangle_other	5.007
r_mcangle_it	4.306
r_mcangle_other	4.306
r_scbond_it	3.375
r_scbond_other	3.375
r_mcbond_it	3.017
r_mcbond_other	3.016
r_angle_refined_deg	1.523
r_angle_other_deg	1.279
r_symmetry_nbd_refined	0.269
r_nbd_other	0.253
r_symmetry_xyhbond_nbd_refined	0.219
r_nbd_refined	0.217
r_symmetry_nbd_other	0.175
r_nbtor_refined	0.166
r_xyhbond_nbd_refined	0.163
r_symmetry_nbtor_other	0.077
r_chiral_restr	0.07
r_ncsr_local_group_2	0.054
r_ncsr_local_group_3	0.053
r_ncsr_local_group_4	0.053
r_ncsr_local_group_5	0.052
r_ncsr_local_group_6	0.051
r_ncsr_local_group_1	0.041
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	7967
Nucleic Acid Atoms
Solvent Atoms	231
Heterogen Atoms	54

Software

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