5ZJ2

Crystal structure of NDM-1 in complex with D-captopril

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.5	295	0.1M Bis-Tris pH5.5, 15% PEG3350, 20mM L-proline

Crystal Properties
Matthews coefficient	Solvent content
2.03	39.53

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 41.698	α = 90
b = 59.892	β = 97.78
c = 42.138	γ = 90

Symmetry
Space Group	P 1 21 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		2016-06-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL17U1	0.97920	SSRF	BL17U1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	1.1	50	99.7	0.08	0.091	0.042	10	4.8		82705

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.1	1.14	100		0.671	0.761	0.354	0.765		4.6

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	3Q6X	1.1	27.95	73459	3859	93.17	0.1368	0.1355	0.1616	RANDOM	23.137

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]
0.06		-0.48	-0.41		0.47

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.125
r_sphericity_free	28.713
r_dihedral_angle_4_deg	19.676
r_dihedral_angle_3_deg	12.974
r_sphericity_bonded	10.601
r_dihedral_angle_1_deg	6.846
r_rigid_bond_restr	3.302
r_angle_refined_deg	1.516
r_angle_other_deg	0.635
r_chiral_restr	0.355
r_bond_refined_d	0.008
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1701
Nucleic Acid Atoms
Solvent Atoms	294
Heterogen Atoms	16

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
PDB_EXTRACT	data extraction
PHASER	phasing