5L8D

X-ray structure of NikA from Escherichia coli in complex with Ru(bis(pyrzol-1-yl)acetate scorpionate)(CO)2Cl

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3MVW

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.7	293	1.8 M ammonium sulfate, 100 mM sodium acetate pH 4.7

Crystal Properties
Matthews coefficient	Solvent content
2.24	45.13

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 86.303	α = 90
b = 93.606	β = 90
c = 124.211	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	93	CCD	ADSC QUANTUM 315r		2015-02-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM30A	0.979763	ESRF	BM30A

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	1.8	46.8	98.8	21.24	4.98		92563

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	3MVW	1.8	46.8	87934	4629	98.77	0.1697	0.1677	0.2082	RANDOM	27.073

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]
1.24			-1.05		-0.19

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.328
r_dihedral_angle_4_deg	16.472
r_dihedral_angle_3_deg	12.213
r_dihedral_angle_1_deg	6.608
r_mcangle_it	3.224
r_mcbond_it	2.434
r_mcbond_other	2.412
r_angle_other_deg	2.347
r_angle_refined_deg	1.898
r_chiral_restr	0.119

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.328
r_dihedral_angle_4_deg	16.472
r_dihedral_angle_3_deg	12.213
r_dihedral_angle_1_deg	6.608
r_mcangle_it	3.224
r_mcbond_it	2.434
r_mcbond_other	2.412
r_angle_other_deg	2.347
r_angle_refined_deg	1.898
r_chiral_restr	0.119
r_bond_refined_d	0.02
r_gen_planes_other	0.013
r_gen_planes_refined	0.011
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7847
Nucleic Acid Atoms
Solvent Atoms	666
Heterogen Atoms	159

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
PHENIX	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.