2VPA

High resolution crystal structure of the antibiotic resistance protein NimA from Deinococcus radiodurans

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1				0.6-0.7 M SODIUM ACETATE AND 0.1 M MES PH 6 OR 0.1 M NA CACODYLATE PH 6.5.

Crystal Properties
Matthews coefficient	Solvent content
1.75	43.35

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 100.037	α = 90
b = 38.951	β = 114.36
c = 59.897	γ = 90

Symmetry
Space Group	C 1 2 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 CCD			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-1		ESRF	ID23-1

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	1.2	20	100	0.09	10.2	5.1		65888			8.16

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	1.2	1.26	100		0.61	2.1	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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1W3O	1.2	20	63865	2004	100	0.142	0.141	0.18	RANDOM	8.82

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]
0.34		0.2	-0.05		-0.12

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.342
r_dihedral_angle_4_deg	13.977
r_dihedral_angle_3_deg	12.756
r_dihedral_angle_1_deg	6.775
r_scangle_it	4.359
r_scbond_it	3.476
r_mcangle_it	2.607
r_mcbond_it	2.125
r_angle_refined_deg	1.734
r_angle_other_deg	1.012
r_xyhbond_nbd_refined	0.258
r_symmetry_vdw_other	0.252
r_nbd_refined	0.245
r_nbd_other	0.223
r_symmetry_hbond_refined	0.223
r_nbtor_refined	0.183
r_chiral_restr	0.116
r_symmetry_vdw_refined	0.113
r_nbtor_other	0.091
r_bond_refined_d	0.02
r_gen_planes_refined	0.011
r_gen_planes_other	0.003
r_bond_other_d	0.002
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1637
Nucleic Acid Atoms
Solvent Atoms	406
Heterogen Atoms	10

Software

Software
Software Name	Purpose
REFMAC	refinement
SCALA	data scaling