2CA9

apo-NIKR from helicobacter pylori in closed trans-conformation

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		4.8		0.9-1 M NA-FORMATE, O.1 M NA-CITRATE PH 4

Crystal Properties
Matthews coefficient	Solvent content
2.4	49.1

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 71.055	α = 90
b = 71.055	β = 90
c = 229.023	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 ID14-1		ESRF	ID14-1

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	2.05	61.55	99.6	0.08	8	5.4		24159			24.8

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	2.05	2.16	99.6		0.44	1.7	5.5

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 (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.	2.05	61.55	21171	1140	99.3	0.201	0.199	0.2	0.25	0.25	RANDOM	29.66

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]
-0.02	-0.01		-0.02		0.03

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.215
r_dihedral_angle_4_deg	22.545
r_dihedral_angle_3_deg	17.517
r_dihedral_angle_1_deg	6.913
r_scangle_it	5.163
r_scbond_it	3.34
r_mcangle_it	2.338
r_angle_refined_deg	1.673
r_mcbond_it	1.518
r_symmetry_hbond_refined	0.343
r_nbtor_refined	0.304
r_symmetry_vdw_refined	0.245
r_nbd_refined	0.232
r_xyhbond_nbd_refined	0.176
r_chiral_restr	0.134
r_bond_refined_d	0.018
r_gen_planes_refined	0.007
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_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	2171
Nucleic Acid Atoms
Solvent Atoms	127
Heterogen Atoms	39

Software

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