2CAD

NikR from Helicobacter pylori in closed trans-conformation and nickel bound to 2F, 2X and 2I sites.

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		NIKR FROM HELICOBACTER PYLORI SOLVED BY SAD METHOD USING MERCURY DERIVATIVE.

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		4.6		0.9-1.0 M NA-FORMATE, 0.1 M NA-CITRATE PH 4.0. CRYSTAL WAS SOAKED IN MOTHER LIQUOR WITH 30% GLYCEROL AND 0.1 M NICKEL SULFATE DURING ONE DAY.

Crystal Properties
Matthews coefficient	Solvent content
2.4	48.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 70.807	α = 90
b = 70.807	β = 90
c = 228.613	γ = 120

Symmetry
Space Group	P 61 2 2

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 ID14-2		ESRF	ID14-2

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	2.3	61.31	100	0.09	6.8	7.9		16035

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	2.3	2.42	100		0.47	1.6	8.2

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	NIKR FROM HELICOBACTER PYLORI SOLVED BY SAD METHOD USING MERCURY DERIVATIVE.	2.3	61.31	15156	795	100	0.204	0.202	0.21	0.257	0.27	RANDOM	30.29

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]
0.1	0.05		0.1		-0.14

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.252
r_dihedral_angle_4_deg	18.686
r_dihedral_angle_3_deg	17.238
r_dihedral_angle_1_deg	7.349
r_scangle_it	2.995
r_scbond_it	1.94
r_mcangle_it	1.683
r_angle_refined_deg	1.586
r_angle_other_deg	1.231
r_mcbond_it	0.979
r_symmetry_vdw_other	0.245
r_chiral_restr	0.228
r_nbd_refined	0.21
r_nbd_other	0.188
r_symmetry_vdw_refined	0.171
r_nbtor_refined	0.169
r_xyhbond_nbd_refined	0.166
r_symmetry_hbond_refined	0.153
r_nbtor_other	0.089
r_bond_refined_d	0.014
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001
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	2107
Nucleic Acid Atoms
Solvent Atoms	118
Heterogen Atoms	46

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALEPACK	data scaling