5NBK

NDM-1 metallo-beta-lactamase: a parsimonious interpretation of the diffraction data

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		298	24 % PEG 1500 AND 0.05 M TBG (SODIUM TARTRATE/BIS - TRIS/GLYCYLGLYCINE) PH 4

Crystal Properties
Matthews coefficient	Solvent content
2.75	55.31

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 108.047	α = 90
b = 108.047	β = 90
c = 92.571	γ = 90

Symmetry
Space Group	P 41 21 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	PIXEL	DECTRIS PILATUS 2M-F		2014-09-13	M	SINGLE WAVELENGTH

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

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.6	46.66	100	999	9.2		17411

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION		FREE R-VALUE	2.6	46.66	16540	871	99.94	0.18298	0.18055	0.22928	copied from 5a5z	42.719

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]
0.09			0.09		-0.19

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.371
r_dihedral_angle_4_deg	20.329
r_dihedral_angle_3_deg	15.052
r_dihedral_angle_1_deg	6.626
r_long_range_B_refined	3.989
r_long_range_B_other	3.987
r_scangle_other	2.14
r_mcangle_it	1.68
r_mcangle_other	1.68
r_angle_refined_deg	1.504
r_scbond_it	1.353
r_scbond_other	1.34
r_angle_other_deg	1.165
r_mcbond_it	0.988
r_mcbond_other	0.988
r_chiral_restr	0.084
r_bond_refined_d	0.013
r_gen_planes_refined	0.007
r_bond_other_d	0.005
r_gen_planes_other	0.005
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3441
Nucleic Acid Atoms
Solvent Atoms	109
Heterogen Atoms	61

Software

Software
Software Name	Purpose
REFMAC	refinement