2CAJ

NikR from Helicobacter pylori in closed trans-conformation and nickel bound to 4 intermediary sites

X-RAY DIFFRACTION

---

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		5		0.9-1.0 M NA-FORMATE, 0.1M NA-CITRATE PH 4.0. CRYSTAL WAS SOAKED IN MOTHER LIQUOR WITH 30% GLYCEROL AND 0.02 M NICKEL CHLORIDE DURING ONE HOUR.

Crystal Properties
Matthews coefficient	Solvent content
2.5	49.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 71.598	α = 90
b = 71.598	β = 90
c = 228.834	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 ID29		ESRF	ID29

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	2.35	62.02	99.7	0.07	8.4	7.4		15378

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	2.35	2.48	99.7		0.49	1.6	6.7

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	2.35	62.02	14496	788	99.7	0.232	0.23	0.24	0.282	0.29	RANDOM	41.68

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]
-0.23	-0.12		-0.23		0.35

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.57
r_dihedral_angle_4_deg	20.427
r_dihedral_angle_3_deg	17.228
r_dihedral_angle_1_deg	7.334
r_scangle_it	4.135
r_scbond_it	2.477
r_mcangle_it	1.996
r_angle_refined_deg	1.643
r_mcbond_it	1.19
r_angle_other_deg	0.866
r_symmetry_vdw_refined	0.323
r_symmetry_vdw_other	0.322
r_nbd_refined	0.214
r_nbd_other	0.195
r_symmetry_hbond_refined	0.187
r_xyhbond_nbd_refined	0.186
r_mcbond_other	0.185
r_nbtor_refined	0.173
r_nbtor_other	0.092
r_chiral_restr	0.087
r_bond_refined_d	0.017
r_gen_planes_refined	0.006
r_bond_other_d	0.002
r_gen_planes_other	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_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	2085
Nucleic Acid Atoms
Solvent Atoms	64
Heterogen Atoms	39

Software

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