2OWM | pdb_00002owm

Motor domain of Neurospora crassa kinesin-3 (NcKin3)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1I5S	TRUNCATED MODEL DERIVED FROM ADP COMPLEX OF KIF1A (1I5S)

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7.5	293	1.5ul protein solution (50mM phosphate buffer pH 7.5, 150mM sodium chloride, 50uM ATP, 1mM magnesium chloride, EGTA, DTT) mixed with 0.5ul reservoir (0.1M Hepes pH 7.5, 0.2M sodium potassium tartrate, 24% PEG3350) and 0.2ul 0.1M magnesium chloride , VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 7.50

Crystal Properties
Matthews coefficient	Solvent content
2.1	41.49

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 75.945	α = 90
b = 98.408	β = 91.86
c = 111.764	γ = 90

Symmetry
Space Group	P 1 21 1

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	MAR CCD 165 mm		2004-05-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE X13		EMBL/DESY, HAMBURG	X13

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	3.25	111.8	100	0.143	6	3.8		26100

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	3.25	3.31	100		0.705		3.8

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 (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	TRUNCATED MODEL DERIVED FROM ADP COMPLEX OF KIF1A (1I5S)	3.25	111.8	26084	24755	1329	100	0.213	0.21	0.21	0.256	0.25	RANDOM	74.79

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]
1.87		5.06	0.85		-2.4

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.618
r_dihedral_angle_3_deg	22.912
r_dihedral_angle_4_deg	19.541
r_dihedral_angle_1_deg	7.38
r_scangle_it	1.867
r_angle_refined_deg	1.844
r_scbond_it	1.122
r_mcangle_it	0.669
r_symmetry_hbond_refined	0.425
r_mcbond_it	0.386
r_nbtor_refined	0.338
r_symmetry_vdw_refined	0.295
r_nbd_refined	0.261
r_xyhbond_nbd_refined	0.169
r_chiral_restr	0.118
r_metal_ion_refined	0.073
r_bond_refined_d	0.018
r_gen_planes_refined	0.005
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_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10226
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	112

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction