6LIP | pdb_00006lip

Crystal structure of NDM-1 in complex with D-captopril derivative wss0218

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5XP6

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
2.05	39.87

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 41.732	α = 90
b = 59.908	β = 97.37
c = 42.295	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		2017-01-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL17U1	0.97914	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	0.98	50	96	0.066	0.071	0.026	14.1	7.2		113420

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	0.98	1.02	81		0.603	0.665	0.275	0.791		5.6

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	5XP6	0.98	27.93	106562	5472	94.83	0.1261	0.1251	0.1348	0.1443	0.1522	RANDOM	20.823

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]
0.26		-0.57	-0.9		0.76

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.888
r_sphericity_free	22.242
r_dihedral_angle_4_deg	20.415
r_dihedral_angle_3_deg	12.464
r_sphericity_bonded	7.952
r_dihedral_angle_1_deg	6.797
r_rigid_bond_restr	1.666
r_angle_refined_deg	1.445
r_angle_other_deg	1.405
r_chiral_restr	0.171
r_gen_planes_other	0.009
r_bond_refined_d	0.008
r_gen_planes_refined	0.008
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1701
Nucleic Acid Atoms
Solvent Atoms	375
Heterogen Atoms	17

Software

Software
Software Name	Purpose
HKL-2000	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction