5ZGZ | pdb_00005zgz

Crystal structure of NDM-1 at pH7.5 (Imidazole) with 1 molecule 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
2.02	39.12

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 41.492	α = 90
b = 59.826	β = 97.84
c = 42.119	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	99.9	0.095	8.7	6.6		127979

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	99.6		0.386		3.6

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	0.95	33.9	121512	6432	99.91	0.1303	0.13	0.1383	0.1354	0.1447	RANDOM	10.944

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]
-0.01		0.03	-0.57		0.55

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.11
r_dihedral_angle_4_deg	19.702
r_sphericity_free	18.446
r_rigid_bond_restr	13.966
r_dihedral_angle_3_deg	12.247
r_dihedral_angle_1_deg	6.36
r_sphericity_bonded	5.438
r_angle_other_deg	2.396
r_angle_refined_deg	1.274
r_chiral_restr	0.079
r_gen_planes_other	0.032
r_gen_planes_refined	0.011
r_bond_refined_d	0.009
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1697
Nucleic Acid Atoms
Solvent Atoms	344
Heterogen Atoms	11

Software

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