5ZGQ | pdb_00005zgq

Crystal structure of NDM-1 at pH7.5 (Tris-HCl, (NH4)2SO4) in complex with hydrolyzed ampicillin

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	7.5	295	0.1M Tris-HCl pH7.5, 25% PEG 4000, 0.7M (NH4)2SO4, 20mg/ml ampicillin

Crystal Properties
Matthews coefficient	Solvent content
2.03	39.35

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 39.2	α = 90
b = 79.068	β = 90
c = 134.162	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	CCD	ADSC QUANTUM 315r		2011-06-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL17U1	0.97922	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	1.5	50	98.6	0.081	7.6	6.5		66725

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	1.5	1.55	95		0.457		6.3

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	1.5	50	63271	3374	98.55	0.1198	0.118	0.12	0.1536	0.15	RANDOM	18.135

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			0.1		-0.17

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.835
r_sphericity_free	26.07
r_dihedral_angle_4_deg	21.111
r_dihedral_angle_3_deg	11.231
r_dihedral_angle_1_deg	6.214
r_sphericity_bonded	4.731
r_angle_refined_deg	1.326
r_angle_other_deg	0.962
r_rigid_bond_restr	0.928
r_chiral_restr	0.082

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.835
r_sphericity_free	26.07
r_dihedral_angle_4_deg	21.111
r_dihedral_angle_3_deg	11.231
r_dihedral_angle_1_deg	6.214
r_sphericity_bonded	4.731
r_angle_refined_deg	1.326
r_angle_other_deg	0.962
r_rigid_bond_restr	0.928
r_chiral_restr	0.082
r_bond_refined_d	0.009
r_gen_planes_refined	0.006
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3594
Nucleic Acid Atoms
Solvent Atoms	585
Heterogen Atoms	56

Software

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

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.