5W3D | pdb_00005w3d

The structure of kinesin-14 wild-type Ncd-ADP dimer

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1N6M

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.8	291	50 mM sodium phosphate, 7 mM dithiothreitol, 10 mM magnesium chloride, 700 mM sodium chloride, 13% PEG8000 (w/v)

Crystal Properties
Matthews coefficient	Solvent content
2.74	55.16

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 163.271	α = 90
b = 67.249	β = 97.92
c = 94.421	γ = 90

Symmetry
Space Group	C 1 2 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	ADSC QUANTUM 315r		2016-10-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSRRC BEAMLINE BL13B1	1.0	NSRRC	BL13B1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym I (Observed)	Rrim I (All)	Rpim I (All)	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	2.789	93.521	99.1	0.091	0.1	0.041	11.5	5.8	25309	25309

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Rrim I (All)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.79	2.94	94.7		0.533	0.533	0.586	0.24	1.5	5.8	3492

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	1N6M	2.79	46.8	24019	1288	99.03	0.2376	0.2353	0.2356	0.2802	0.2753	RANDOM	80.678

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]
4		4.56	0.83		-5.26

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.438
r_dihedral_angle_3_deg	18.929
r_dihedral_angle_4_deg	18.347
r_dihedral_angle_1_deg	5.851
r_angle_other_deg	3.609
r_angle_refined_deg	1.29
r_chiral_restr	0.074
r_bond_refined_d	0.008
r_gen_planes_refined	0.004
r_gen_planes_other	0.004
r_bond_other_d

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5292
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	56

Software

Software
Software Name	Purpose
REFMAC	refinement
SCALA	data scaling
Coot	model building
PDB_EXTRACT	data extraction
XDS	data reduction
MOLREP	phasing