3QIM | pdb_00003qim

Histidine 416 of the periplamsic binding protein NikA is essential for nickel uptake in Escherichia coli

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1ZLQ	PDB ENTRY 1ZLQ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.7	293	1.6M Ammonium sulfate, 100 mM sodium acetate, pH 4.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.25	45.31

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 86.731	α = 90
b = 94.005	β = 90
c = 124.33	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 210r		2010-06-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM16	0.984	ESRF	BM16

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	2.1	24.84	93	0.06	12.93	2.6		56622		2	27.4

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	PDB ENTRY 1ZLQ	2.1	24.84	56622	2981	100	0.17911	0.17607	0.18	0.2369	0.24	RANDOM	27.411

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]
0.18			-1.49		1.31

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.925
r_dihedral_angle_3_deg	16.186
r_dihedral_angle_4_deg	16.031
r_dihedral_angle_1_deg	6.408
r_scangle_it	3.946
r_scbond_it	2.501
r_angle_refined_deg	1.541
r_mcangle_it	1.518
r_mcbond_it	0.822
r_chiral_restr	0.103

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.925
r_dihedral_angle_3_deg	16.186
r_dihedral_angle_4_deg	16.031
r_dihedral_angle_1_deg	6.408
r_scangle_it	3.946
r_scbond_it	2.501
r_angle_refined_deg	1.541
r_mcangle_it	1.518
r_mcbond_it	0.822
r_chiral_restr	0.103
r_bond_refined_d	0.015
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7897
Nucleic Acid Atoms
Solvent Atoms	506
Heterogen Atoms	120

Software

Software
Software Name	Purpose
MX	data collection
PHASER	phasing
REFMAC	refinement
XDS	data reduction
XDS	data scaling

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.