4FR7 | pdb_00004fr7

Crystal structure of the metallo-beta-lactamase VIM-31 in its reduced form at 1.61 A

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1KO3	PDB entry 1ko3

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	296	VIM-31 (17 mg/ml) 1:1 dilution with the condition 0.3 M sodium acetate, 0.1 M Tris-HCl pH 8.5, 20 % PEG4000 1.0 mM TCEP, VAPOR DIFFUSION, SITTING DROP, temperature 296K

Crystal Properties
Matthews coefficient	Solvent content
1.87	34.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 64.6	α = 90
b = 74.39	β = 90
c = 78.72	γ = 90

Symmetry
Space Group	I 2 2 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	IMAGE PLATE	MAR scanner 345 mm plate		2012-05-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	ENRAF-NONIUS FR591	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	1.61	54.068	97.9	0.059	15.5	4.9	24650	24650

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.6	1.69	87.5		0.404	0.404	1.9	4.5	3177

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 1ko3	1.61	54.068	24650	24650	1257	99.06	0.1493	0.1474	0.16	0.1856	0.19	RANDOM	23.0752

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]
6.83			-0.5		-6.33

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.832
r_dihedral_angle_4_deg	20.54
r_dihedral_angle_3_deg	12.302
r_dihedral_angle_1_deg	6.45
r_angle_refined_deg	1.312
r_angle_other_deg	0.856
r_chiral_restr	0.083
r_bond_refined_d	0.016
r_bond_other_d	0.014
r_gen_planes_refined	0.014

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.832
r_dihedral_angle_4_deg	20.54
r_dihedral_angle_3_deg	12.302
r_dihedral_angle_1_deg	6.45
r_angle_refined_deg	1.312
r_angle_other_deg	0.856
r_chiral_restr	0.083
r_bond_refined_d	0.016
r_bond_other_d	0.014
r_gen_planes_refined	0.014
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1734
Nucleic Acid Atoms
Solvent Atoms	215
Heterogen Atoms	12

Software

Software
Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345dtb	data collection
MOSFLM	data reduction
MOLREP	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.