8SP2

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

X-RAY DIFFRACTION

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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	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2.2	74.608	224388	11220	91.205	0.215	0.2125	0.257	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