7WZU

Crystal structure of metallo-beta-lactamase IMP-6.

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1DD6

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6	297	Hepes, sodium acetate, sodium citrate, PEG 4000

Crystal Properties
Matthews coefficient	Solvent content
2.88	57.26

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 49.799	α = 83.446
b = 76.098	β = 75.317
c = 82.114	γ = 74.063

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	CCD	ADSC QUANTUM 315r		2013-11-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-5A	1.0000	Photon Factory	BL-5A

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	1.954	50	92.9	0.089	20	3		75127

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	1.96	1.99	66.4		0.172	3.1	2.2

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	1DD6	1.954	35.415	75080	3754	92.517	0.192	0.1899	0.2263	31.882

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]
0.001		0.001			-0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.138
r_dihedral_angle_4_deg	22.248
r_dihedral_angle_3_deg	14.841
r_dihedral_angle_1_deg	7.053
r_lrange_other	6.008
r_lrange_it	6.006
r_scangle_it	3.87
r_scangle_other	3.87
r_mcangle_other	3.395
r_mcangle_it	3.394
r_scbond_it	2.317
r_scbond_other	2.315
r_mcbond_it	2.05
r_mcbond_other	2.047
r_angle_refined_deg	1.345
r_angle_other_deg	1.191
r_nbd_refined	0.196
r_nbd_other	0.193
r_symmetry_nbd_refined	0.172
r_symmetry_nbd_other	0.17
r_nbtor_refined	0.158
r_xyhbond_nbd_refined	0.135
r_symmetry_xyhbond_nbd_refined	0.113
r_symmetry_nbtor_other	0.074
r_chiral_restr	0.062
r_metal_ion_refined	0.051
r_bond_refined_d	0.006
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6780
Nucleic Acid Atoms
Solvent Atoms	288
Heterogen Atoms	8

Software

Software
Software Name	Purpose
HKL-2000	data collection
HKL-2000	data scaling
AMoRE	phasing
REFMAC	refinement
PHENIX	refinement
Coot	model building