5ZIO | pdb_00005zio

Crystal structure of NDM-1 in complex with L-captopril

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 Bis-Tris pH5.5, 15% PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.03	39.53

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 41.506	α = 90
b = 59.948	β = 98.06
c = 41.904	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		2012-01-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL17U1	0.97924	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	0.98	50	90.2	0.073	11.8	7		104952

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	0.98	1.02	63.4		0.268		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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	3Q6X	0.98	41.13	99642	5281	90.2	0.1242	0.1235	0.124	0.1373	0.1382	RANDOM	14.192

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]
-0.14		0.14	-0.27		0.37

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.75
r_dihedral_angle_4_deg	15.438
r_dihedral_angle_3_deg	11.718
r_sphericity_bonded	7.493
r_dihedral_angle_1_deg	6.381
r_rigid_bond_restr	1.888
r_angle_refined_deg	1.261
r_angle_other_deg	0.745
r_chiral_restr	0.076
r_bond_refined_d	0.009
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1697
Nucleic Acid Atoms
Solvent Atoms	281
Heterogen Atoms	16

Software

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