8SP2 | pdb_00008sp2

Crystal structure of metformin hydrolase (MfmAB) from Pseudomonas mendocina sp. MET-2 apo form

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold	A0A2S0XPN7	used for modelling MfmA
in silico model	AlphaFold	A0A316GGX0	used for modelling MfmB

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	291	1 uL 10 mg/mL protein + 1 uL 13.5% w/v PEG3350, 0.1 M Bis-Tris propane, 0.2 M NaNO3, pH 7.5

Crystal Properties
Matthews coefficient	Solvent content
2.68	54.07

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 103.53	α = 93.429
b = 107.88	β = 97.625
c = 114.51	γ = 98.105

Symmetry
Space Group	P 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	PIXEL	DECTRIS EIGER X 16M		2022-07-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 24-ID-E	0.97918	APS	24-ID-E

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	2.2	80	91.2	0.999	12.75	2.0558		224389

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	2.2	2.3	89		0.745	1.59

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	THROUGHOUT	2.2	74.608	224388	11220	91.205	0.215	0.2125	0.22	0.257	0.26	50.927

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]
0.408	-0.565	-0.543	0.2	0.612	-0.402

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	17.624
r_dihedral_angle_6_deg	15.9
r_dihedral_angle_2_deg	7.954
r_lrange_it	7.761
r_lrange_other	7.752
r_dihedral_angle_1_deg	7.219
r_scangle_it	4.558
r_scangle_other	4.558
r_mcangle_it	4.253
r_mcangle_other	4.253
r_scbond_it	2.878
r_scbond_other	2.878
r_mcbond_it	2.77
r_mcbond_other	2.77
r_angle_refined_deg	1.314
r_angle_other_deg	0.457
r_nbd_other	0.22
r_nbd_refined	0.217
r_symmetry_nbd_other	0.206
r_nbtor_refined	0.181
r_symmetry_nbd_refined	0.177
r_xyhbond_nbd_refined	0.175
r_symmetry_xyhbond_nbd_refined	0.142
r_symmetry_xyhbond_nbd_other	0.085
r_symmetry_nbtor_other	0.08
r_chiral_restr	0.068
r_bond_refined_d	0.005
r_gen_planes_refined	0.005
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	31104
Nucleic Acid Atoms
Solvent Atoms	910
Heterogen Atoms	8

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing
Coot	model building