3NWN | pdb_00003nwn

Crystal structure of the human KIF9 motor domain in complex with ADP

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1GOJ	pdb entry 1GOJ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	291	1.5M ammonium sulfate, 0.1M TRIS, pH 8.5, vapor diffusion, sitting drop, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.24	45.19

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 90.443	α = 90
b = 90.443	β = 90
c = 76.38	γ = 120

Symmetry
Space Group	P 63

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray		IMAGE PLATE			2006-10-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-E	1.54178

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	2	30	99.1	0.059	18.2	5.2		46976

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)
	2	2.07		99.5	0.411		5.2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	pdb entry 1GOJ	2	29.173	22881	1145	95.072	0.226	0.2238	0.23	0.277	0.28	random	28.19

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]
-0.349	-0.175		-0.349		0.524

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	41.365
r_dihedral_angle_4_deg	17.125
r_dihedral_angle_3_deg	13.771
r_dihedral_angle_1_deg	6.069
r_mcangle_it	3.679
r_scangle_it	3.514
r_mcbond_it	2.81
r_scbond_it	2.659
r_angle_refined_deg	1.414
r_angle_other_deg	1.4
r_mcbond_other	0.59
r_symmetry_vdw_other	0.208
r_symmetry_vdw_refined	0.206
r_nbd_other	0.2
r_nbd_refined	0.186
r_nbtor_refined	0.17
r_xyhbond_nbd_refined	0.156
r_symmetry_hbond_refined	0.099
r_chiral_restr	0.081
r_nbtor_other	0.079
r_metal_ion_refined	0.058
r_bond_refined_d	0.017
r_gen_planes_refined	0.005
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2400
Nucleic Acid Atoms
Solvent Atoms	85
Heterogen Atoms	37

Software

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