6KXI | pdb_00006kxi

Crystal Structure Of NDM-1 Metallo-beta-lactamase In Complex With Inhibitor NO9

X-RAY DIFFRACTION

---

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
2.04	39.76

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 70.55	α = 90
b = 73.66	β = 90
c = 77.75	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 PILATUS 2M		2017-04-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE AR-NE3A	1.00	Photon Factory	AR-NE3A

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	1.38	42.624	100	0.108	16.9	12		83907

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	1.38	1.45	100		0.205		12.1

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	1.38	42.624	83827	4159	99.993	0.137	0.1362	0.14	0.1573	0.16	11.041

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]
0.093			-0.105		0.012

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.251
r_dihedral_angle_4_deg	23.865
r_dihedral_angle_3_deg	14.002
r_dihedral_angle_1_deg	13.17
r_dihedral_angle_other_3_deg	10.542
r_lrange_it	5.179
r_lrange_other	5.062
r_scangle_other	3.214
r_scangle_it	3.212
r_mcangle_it	2.347
r_mcangle_other	2.347
r_scbond_other	2.114
r_scbond_it	2.113
r_angle_refined_deg	1.569
r_angle_other_deg	1.489
r_mcbond_it	1.433
r_mcbond_other	1.427
r_nbd_other	0.218
r_nbd_refined	0.214
r_symmetry_nbd_refined	0.208
r_symmetry_nbd_other	0.195
r_nbtor_refined	0.169
r_symmetry_xyhbond_nbd_refined	0.161
r_xyhbond_nbd_refined	0.15
r_symmetry_nbtor_other	0.086
r_chiral_restr	0.077
r_symmetry_xyhbond_nbd_other	0.076
r_bond_refined_d	0.019
r_gen_planes_refined	0.006
r_gen_planes_other	0.001
r_bond_other_d

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3466
Nucleic Acid Atoms
Solvent Atoms	628
Heterogen Atoms	54

Software

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