5O2E

Crystal structure of NDM-1 in complex with hydrolyzed cefuroxime - new refinement

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6	295	30% (w/v) PEG3350, 0.1M Bis-Tris pH 6.0 and 0.2 M lithium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.01	38.67

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 39.18	α = 90
b = 78.89	β = 90
c = 133.06	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		2012-04-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL17B1	0.9791	SSRF	BL17B1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.3	29.36	98.8				93575

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	1.3	29.36	88894	4618	91.38	0.10251	0.10096	0.13265	copied from 4rl0	14.575

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]
-0.08			0.05		0.03

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.98
r_sphericity_free	29.013
r_dihedral_angle_4_deg	19.274
r_dihedral_angle_3_deg	11.643
r_sphericity_bonded	9.444
r_dihedral_angle_1_deg	6.299
r_long_range_B_refined	4.265
r_long_range_B_other	4.264
r_scangle_other	3.376
r_scbond_other	3.059
r_scbond_it	3.058
r_mcangle_it	2.193
r_mcangle_other	2.193
r_mcbond_other	1.875
r_mcbond_it	1.874
r_rigid_bond_restr	1.658
r_angle_refined_deg	1.625
r_angle_other_deg	0.99
r_chiral_restr	0.104
r_bond_refined_d	0.013
r_gen_planes_refined	0.009
r_bond_other_d	0.002
r_gen_planes_other	0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3549
Nucleic Acid Atoms
Solvent Atoms	676
Heterogen Atoms	63

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing