6LBL

Crystal structure of IMP-1 metallo-beta-lactamase in complex with NO9 inhibitor

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5EV6

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	30% PEG 3350, 0.2M sodium acetate, 0.1M HEPES

Crystal Properties
Matthews coefficient	Solvent content
2.03	39.53

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 35.92	α = 90
b = 56.61	β = 90
c = 100.62	γ = 90

Symmetry
Space Group	P 21 21 21

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		2017-03-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	AichiSR BEAMLINE BL2S1	1.12	AichiSR	BL2S1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.68	56.61	99.7	0.067	18.9	8.8		24088

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.68	1.77	99.9		0.281		8.9

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	THROUGHOUT	5ev6	1.68	49.386	24038	1187	99.59	0.16	0.1577	0.208	25.78

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]
-0.257			1.241		-0.984

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.428
r_dihedral_angle_4_deg	20.678
r_dihedral_angle_3_deg	14.929
r_dihedral_angle_1_deg	7.739
r_lrange_other	7.268
r_lrange_it	7.265
r_dihedral_angle_other_3_deg	6.705
r_scangle_it	6.054
r_scangle_other	6.051
r_scbond_it	4.259
r_scbond_other	4.259
r_mcangle_it	3.569
r_mcangle_other	3.568
r_mcbond_it	2.639
r_mcbond_other	2.632
r_angle_refined_deg	1.528
r_angle_other_deg	1.338
r_symmetry_xyhbond_nbd_refined	0.255
r_nbd_other	0.227
r_nbd_refined	0.22
r_symmetry_nbd_other	0.199
r_symmetry_nbd_refined	0.188
r_nbtor_refined	0.169
r_xyhbond_nbd_refined	0.168
r_symmetry_xyhbond_nbd_other	0.111
r_chiral_restr	0.079
r_symmetry_nbtor_other	0.079
r_metal_ion_refined	0.044
r_bond_refined_d	0.008
r_gen_planes_refined	0.007
r_bond_other_d
r_gen_planes_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1728
Nucleic Acid Atoms
Solvent Atoms	225
Heterogen Atoms	17

Software

Software
Software Name	Purpose
REFMAC	refinement
iMOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing