8SNF

Crystal structure of metformin hydrolase (MfmAB) from Pseudomonas mendocina sp. MET-2 with Ni2+2 bound

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 14.5% w/v PEG3350, 0.1 M Bis-Tris propane, 0.2 M NaNO3, pH 7.5

Crystal Properties
Matthews coefficient	Solvent content
2.69	54.29

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 83.4	α = 115.5
b = 96.4	β = 106.2
c = 96.7	γ = 101.1

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 PILATUS3 6M		2023-02-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-D	1.0332	APS	23-ID-D

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	2.3	80	91.3	0.998	13.3	2.408		99100

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	2.3	2.4	88.6		0.96	3.07

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	2.3	19.865	99098	5056	91.623	0.174	0.1719	0.2194	76.693

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]
-3.769	2.669	3.824	-2.678	2.882	-0.966

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	17.418
r_dihedral_angle_6_deg	15.517
r_lrange_other	10.237
r_lrange_it	10.232
r_scangle_it	8.718
r_scangle_other	8.718
r_dihedral_angle_2_deg	8.088
r_dihedral_angle_1_deg	7.287
r_mcangle_it	6.472
r_mcangle_other	6.472
r_scbond_it	6.167
r_scbond_other	6.167
r_mcbond_it	4.992
r_mcbond_other	4.992
r_angle_refined_deg	1.449
r_angle_other_deg	0.493
r_nbd_refined	0.221
r_symmetry_nbd_other	0.205
r_symmetry_xyhbond_nbd_refined	0.195
r_symmetry_nbd_refined	0.192
r_nbtor_refined	0.184
r_nbd_other	0.179
r_xyhbond_nbd_refined	0.171
r_symmetry_nbtor_other	0.081
r_symmetry_xyhbond_nbd_other	0.075
r_chiral_restr	0.072
r_bond_refined_d	0.007
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	15458
Nucleic Acid Atoms
Solvent Atoms	330
Heterogen Atoms	4

Software

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