3DC4 | pdb_00003dc4

Crystal structure of the Drosophila kinesin family member NOD in complex with ADP

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	277	0.1 MES, 15% PEG 20000, Se-MET Derivative, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
2	VAPOR DIFFUSION, HANGING DROP	6.5	277	0.1 MES, 15% PEG 20000, NATIVE PROTEIN, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 47.829	α = 90
b = 75.715	β = 90
c = 94.58	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		CCD	ADSC	TOROIDAL FOCUSING MIRROR	2007-04-07	M	MAD
2	1	x-ray		CCD	ADSC	TOROIDAL FOCUSING MIRROR	2007-07-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X6A	0.9790, 0.9796, 0.9184	NSLS	X6A
2	SYNCHROTRON	NSLS BEAMLINE X6A	0.9791	NSLS	X6A

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
1,2	1.9	19	98.6	0.057	8.2	22.77	4.81		27088	1	-3	30.315

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)
	1.9	2	98.8		0.342	35.4	4.9	4.88	18583

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MAD, MR	THROUGHOUT	1.9	19	27088	1320	97.8	0.227	0.22	0.255	0.25	RANDOM	34.2

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]
2.81			-7		4.18

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	23.8
c_improper_angle_d	2.27
c_angle_deg	1.6
c_bond_d	0.006
c_mcbond_it
c_mcangle_it
c_scbond_it
c_scangle_it

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2247
Nucleic Acid Atoms
Solvent Atoms	312
Heterogen Atoms	28

Software

Software
Software Name	Purpose
XSCALE	data scaling
CNS	refinement
SOLVE	phasing
RESOLVE	phasing
PDB_EXTRACT	data extraction
CNS	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.