6KZL | pdb_00006kzl

Crystal Structure Of NDM-1 Metallo-beta-lactamase In Complex With Inhibitor X2

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4EYB

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	0.2M Ammonium Sulfate, 0.1M Bis-Tris [pH 6.1], 25% PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2	38.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 70.72	α = 90
b = 74.04	β = 90
c = 77.43	γ = 90

Symmetry
Space Group	P 21 21 21

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 PILATUS3 S 6M		2017-12-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-5A	1.00	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	1.76	77.43	100	0.12	14.8	10.3		40824

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	1.76	1.86	99.9		0.474		9.5

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	4eyb	1.763	53.513	40758	2034	99.971	0.15	0.148	0.16	0.1916	0.2	20.359

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]
0.145			-0.392		0.247

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.304
r_dihedral_angle_4_deg	19.688
r_dihedral_angle_3_deg	14.762
r_dihedral_angle_1_deg	8.088
r_lrange_it	5.691
r_lrange_other	5.638
r_scangle_it	3.991
r_scangle_other	3.991
r_scbond_it	2.732
r_scbond_other	2.732
r_mcangle_other	2.696
r_mcangle_it	2.692
r_mcbond_it	1.896
r_mcbond_other	1.89
r_angle_refined_deg	1.365
r_angle_other_deg	1.334
r_nbd_other	0.237
r_symmetry_nbd_refined	0.235
r_nbd_refined	0.207
r_symmetry_nbd_other	0.201
r_symmetry_xyhbond_nbd_refined	0.197
r_xyhbond_nbd_refined	0.164
r_nbtor_refined	0.158
r_symmetry_nbtor_other	0.081
r_metal_ion_refined	0.081
r_chiral_restr	0.063
r_bond_refined_d	0.005
r_gen_planes_refined	0.005
r_gen_planes_other	0.001
r_bond_other_d

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3537
Nucleic Acid Atoms
Solvent Atoms	478
Heterogen Atoms	65

Software

Software
Software Name	Purpose
REFMAC	refinement
iMOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing