5ZGW

Crystal structure of NDM-1 at pH7.5 with 1 molecule per asymmetric unit (crystallized at succinate pH5.5 and soaked at succinate pH7.5)

X-RAY DIFFRACTION

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 sodium succinate pH5.5, 20% PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2	38.55

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 41.456	α = 90
b = 59.905	β = 98.14
c = 41.74	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		2012-03-27	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	0.95	50	98.7	0.108	10.6	7.1		125133

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	0.95	0.98	96.1		0.325		3.9

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	0.95	41.32	118845	6266	98.64	0.1293	0.1287	0.1404	RANDOM	9.555

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]
-0.34		0.29	-0.67		1.09

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.486
r_dihedral_angle_4_deg	20.198
r_sphericity_free	17.146
r_dihedral_angle_3_deg	11.069
r_dihedral_angle_1_deg	6.282
r_sphericity_bonded	5.693
r_rigid_bond_restr	1.739
r_angle_refined_deg	1.234
r_angle_other_deg	0.843
r_chiral_restr	0.076

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.486
r_dihedral_angle_4_deg	20.198
r_sphericity_free	17.146
r_dihedral_angle_3_deg	11.069
r_dihedral_angle_1_deg	6.282
r_sphericity_bonded	5.693
r_rigid_bond_restr	1.739
r_angle_refined_deg	1.234
r_angle_other_deg	0.843
r_chiral_restr	0.076
r_bond_refined_d	0.007
r_gen_planes_refined	0.006
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1701
Nucleic Acid Atoms
Solvent Atoms	287
Heterogen Atoms	33

Software

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.