Experiment: 3BKF

Zinc-bound C-terminal Domain of NikR

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1Q5Y	MONOMER OF PDB 1Q5Y

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6	298	0.1M Bis-Tris, 0.2M Ammonium Sulfate, 25% w/v PEG 3350, pH 6.0, vapor diffusion, hanging drop, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
1.98	37.88

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 46.22	α = 90
b = 46.22	β = 90
c = 124.9	γ = 120

Symmetry
Space Group	P 62 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	MARMOSAIC 325 mm CCD		2006-07-09	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2	1.2829, 1.0	SSRL	BL9-2

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	1.9	40	99.5	0.52	28.1	9.8		6755

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.9	2			0.345	3.4	6	957

Refinement

Statistics
Diffraction ID	Structure Solution 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		MONOMER OF PDB 1Q5Y	1.9	40	6789	6755	564	99.3	0.251	0.251	0.25	0.2689	0.273	0.268	RANDOM	45.545

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]
2.155	-2.315		2.155		-4.311

RMS Deviations
Key	Refinement Restraint Deviation
c_scangle_it	3.767
c_mcangle_it	3.63
c_scbond_it	2.298
c_mcbond_it	2.201

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	508
Nucleic Acid Atoms
Solvent Atoms	22
Heterogen Atoms	2

Software

Software
Software Name	Purpose
SCALA	data processing
CNS	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
MOSFLM	data reduction
SCALA	data scaling
CNS	phasing