7O5Q | pdb_00007o5q

Crystal Structure of a Class D Carbapenemase Complexed with Hydrolyzed Oxacillin

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		291	0.1M HEPES pH 8.0, 10% PEG 8000, 10% 1-BUTANOL mixed with the 10 mg/mL protein stock at 1:1 ratio.

Crystal Properties
Matthews coefficient	Solvent content
2.71	54.69

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 47.053	α = 90
b = 126.902	β = 98.289
c = 111.201	γ = 90

Symmetry
Space Group	P 1 21 1

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		2020-06-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL17U1	0.979150	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	1.85	19.81	99.9	0.997	10	6.9		109814

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			0.725	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	1.85	19.807	109782	5465	99.864	0.175	0.1731	0.18	0.2111	0.22	27.894

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]
3.963		0.53	-2.548		-1.505

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.164
r_dihedral_angle_4_deg	17.442
r_dihedral_angle_3_deg	13.699
r_dihedral_angle_1_deg	6.039
r_lrange_it	5.858
r_lrange_other	5.778
r_scangle_it	4.775
r_scangle_other	4.775
r_scbond_it	3.092
r_scbond_other	3.092
r_mcangle_it	2.92
r_mcangle_other	2.919
r_mcbond_it	2.11
r_mcbond_other	2.109
r_angle_refined_deg	1.631
r_angle_other_deg	1.31
r_nbd_other	0.297
r_nbd_refined	0.205
r_symmetry_nbd_refined	0.179
r_symmetry_xyhbond_nbd_refined	0.165
r_symmetry_nbd_other	0.162
r_nbtor_refined	0.158
r_xyhbond_nbd_refined	0.15
r_chiral_restr_other	0.09
r_chiral_restr	0.081
r_symmetry_nbtor_other	0.075
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	7932
Nucleic Acid Atoms
Solvent Atoms	703
Heterogen Atoms	167

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
MOLREP	phasing