6KXO

Crystal Structure Of VIM-2 Metallo-beta-lactamase In Complex With Inhibitor NO9

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4NQ2

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	0.2M magnesium formate dihydrate, 25% PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.04	39.58

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 101.501	α = 90
b = 79.21	β = 130.13
c = 67.66	γ = 90

Symmetry
Space Group	C 1 2 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	CCD	ADSC QUANTUM 315r		2017-05-19	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	1.49	55.43	99.3	0.079	15.3	7.1		66587

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	1.49	1.57	99.5		0.319		6.9

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	4nq2	1.49	51.487	66585	3468	99.73	0.147	0.1456	0.1691	12.17

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]
0.416		0.025	-0.476		0.007

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.668
r_dihedral_angle_4_deg	19.898
r_dihedral_angle_3_deg	12.264
r_dihedral_angle_1_deg	7.423
r_lrange_it	4.945
r_lrange_other	4.827
r_scangle_it	3.297
r_scangle_other	3.297
r_scbond_it	2.273
r_scbond_other	2.272
r_dihedral_angle_other_3_deg	2.073
r_mcangle_it	1.849
r_mcangle_other	1.848
r_angle_refined_deg	1.599
r_angle_other_deg	1.428
r_mcbond_it	1.258
r_mcbond_other	1.257
r_nbd_other	0.26
r_symmetry_nbd_refined	0.214
r_nbd_refined	0.202
r_symmetry_nbd_other	0.202
r_symmetry_xyhbond_nbd_refined	0.178
r_nbtor_refined	0.165
r_xyhbond_nbd_refined	0.157
r_metal_ion_refined	0.114
r_symmetry_nbtor_other	0.08
r_chiral_restr	0.068
r_bond_refined_d	0.008
r_gen_planes_refined	0.006
r_bond_other_d
r_gen_planes_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3492
Nucleic Acid Atoms
Solvent Atoms	637
Heterogen Atoms	64

Software

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