5ZH1 | pdb_00005zh1

Crystal structure of NDM-1 at pH7.5 (Imidazole) with 2 molecules per asymmetric unit

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 imidazole pH7.5, 20% PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
1.9	35.42

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 40.54	α = 90
b = 73.619	β = 97.88
c = 66.055	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		2012-07-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL17U1	0.93924	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	1.05	50	94.8	0.065	10.1	7.5		168917

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	1.05	1.09	91.7		0.495		7.5

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 (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	1.05	32.75	129414	6834	77.18	0.1277	0.1267	0.1263	0.1465	0.1463	RANDOM	23.372

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]
-0.02		0.76	-0.75		0.64

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.618
r_sphericity_free	31.146
r_dihedral_angle_4_deg	18.758
r_dihedral_angle_3_deg	12.223
r_sphericity_bonded	8.6
r_dihedral_angle_1_deg	6.211
r_rigid_bond_restr	1.387
r_angle_refined_deg	1.247
r_angle_other_deg	1.02
r_chiral_restr	0.075
r_bond_refined_d	0.007
r_gen_planes_refined	0.006
r_bond_other_d	0.004
r_gen_planes_other	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3580
Nucleic Acid Atoms
Solvent Atoms	549
Heterogen Atoms	16

Software

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