6YI4

Structure of IMP-13 metallo-beta-lactamase complexed with citrate anion

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6R78

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		298	Ammonium acetate, Na citrate, PEG 4000

Crystal Properties
Matthews coefficient	Solvent content
2.49	50.58

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 47.675	α = 90
b = 90.467	β = 100.853
c = 88.522	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	90	PIXEL	DECTRIS PILATUS 2M-F		2020-02-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06DA	1	SLS	X06DA

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	1.7	46.866	99.74	0.998	6.4	5.7		80810

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	1.7	1.76			0.72

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	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	6R78	1.7	46.866	80810	3820	99.719	0.182	0.18	0.2129	30.136

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]
-0.139		-0.443	1.654		-1.253

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.901
r_dihedral_angle_3_deg	15.744
r_dihedral_angle_4_deg	14.311
r_lrange_it	7.045
r_lrange_other	6.995
r_dihedral_angle_1_deg	6.818
r_scangle_it	5.464
r_scangle_other	5.464
r_mcangle_other	3.841
r_mcangle_it	3.839
r_scbond_it	3.67
r_scbond_other	3.67
r_mcbond_it	2.833
r_mcbond_other	2.826
r_angle_other_deg	2.342
r_angle_refined_deg	1.67
r_symmetry_xyhbond_nbd_other	0.477
r_symmetry_xyhbond_nbd_refined	0.357
r_metal_ion_refined	0.269
r_nbd_other	0.258
r_nbd_refined	0.232
r_symmetry_nbd_other	0.222
r_xyhbond_nbd_refined	0.222
r_symmetry_nbd_refined	0.195
r_nbtor_refined	0.167
r_chiral_restr	0.095
r_symmetry_nbtor_other	0.076
r_bond_other_d	0.035
r_gen_planes_other	0.014
r_bond_refined_d	0.011
r_gen_planes_refined	0.01

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5139
Nucleic Acid Atoms
Solvent Atoms	407
Heterogen Atoms	64

Software

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