5ZJC | pdb_00005zjc

Crystal structure of NDM-1 in complex with D-captopril derivative CY41

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3Q6X

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.5	295	0.1M Bis-Tris pH5.5, 15% PEG 3350, 20mM L-proline

Crystal Properties
Matthews coefficient	Solvent content
2.03	39.37

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 41.61	α = 90
b = 59.98	β = 97.88
c = 42.067	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		2013-09-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL17U1	0.97930	SSRF	BL17U1

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	0.96	50	96.1	0.064	22.1	6.2		119689

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	0.96	0.99	66.9		0.334		3.2

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 (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	3Q6X	0.96	41.67	100828	5330	86.22	0.1289	0.1281	0.1286	0.1455	0.145	RANDOM	22.936

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]
0.07		-0.41	-0.52		0.54

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.213
r_dihedral_angle_4_deg	18.48
r_sphericity_free	17.167
r_dihedral_angle_3_deg	12.01
r_dihedral_angle_1_deg	6.526
r_sphericity_bonded	4.907
r_angle_refined_deg	1.376
r_rigid_bond_restr	1.064
r_angle_other_deg	0.984
r_chiral_restr	0.085
r_bond_refined_d	0.008
r_gen_planes_refined	0.007
r_bond_other_d	0.003
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1697
Nucleic Acid Atoms
Solvent Atoms	295
Heterogen Atoms	16

Software

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