3BKT | pdb_00003bkt

Copper-bound C-terminal Domain of NikR

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1Q5Y	The tetramer of nickel-bound c-terminal domain of NikR, 1Q5Y

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	298	0.2M Na Tartrate, 20% PEG 3350, pH 8.0, vapor diffusion, hanging drop, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
1.89	34.82

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 45.949	α = 90
b = 78.442	β = 90
c = 81.46	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 315		2004-02-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 8-BM	0.9791	APS	8-BM

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	1.5	50	97.9	0.059	0.057	16.9	8.1	47685	46684

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.5	1.55	85.2		0.263	0.254	5.3	6.1	4006

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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		THROUGHOUT	The tetramer of nickel-bound c-terminal domain of NikR, 1Q5Y	1.5	15.17	46684	46629	2360	97.94	0.198	0.198	0.196	0.2	0.227	0.23	RANDOM	16.047

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]
0.04			-0.02		-0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.752
r_dihedral_angle_4_deg	17.066
r_dihedral_angle_3_deg	14.148
r_sphericity_free	6.882
r_dihedral_angle_1_deg	5.878
r_scangle_it	3.8
r_sphericity_bonded	3.062
r_scbond_it	2.808
r_rigid_bond_restr	2.663
r_mcangle_it	2.105
r_mcbond_it	1.403
r_angle_refined_deg	1.346
r_angle_other_deg	0.877
r_mcbond_other	0.527
r_symmetry_hbond_refined	0.219
r_nbd_refined	0.209
r_nbd_other	0.187
r_symmetry_vdw_other	0.183
r_xyhbond_nbd_refined	0.179
r_nbtor_refined	0.17
r_symmetry_vdw_refined	0.159
r_nbtor_other	0.086
r_chiral_restr	0.085
r_metal_ion_refined	0.04
r_bond_refined_d	0.011
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2618
Nucleic Acid Atoms
Solvent Atoms	171
Heterogen Atoms	4

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345dtb	data collection
XFIT	data reduction