3WPN | pdb_00003wpn

Kinesin spindle protein Eg5 in complex with ATP-competitive inhibitor PVZB1194

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1Q0B	PDB ENTRY 1Q0B

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6	277	19% PEG3350, 0.1M MES, 0.2M NaNO3, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.36	47.91

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 71.912	α = 90
b = 95.425	β = 90
c = 59.015	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	95	CCD	ADSC QUANTUM 315r	mirror	2012-11-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-17A	0.9800	Photon Factory	BL-17A

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	2.8	20	98.2	0.084	38.7	6.4		10303			65.4

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	2.8	2.85	98.8		0.454	6.8

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	PDB ENTRY 1Q0B	2.8	19.88	9251	1017	97.84	0.23121	0.22455	0.22	0.29008	0.28	RANDOM	65.804

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]
-0.56			0.19		0.37

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	41.685
r_dihedral_angle_3_deg	17.394
r_dihedral_angle_4_deg	16.35
r_long_range_B_refined	11.613
r_long_range_B_other	11.61
r_scangle_other	7.512
r_mcangle_it	6.674
r_dihedral_angle_1_deg	5.421
r_scbond_other	4.709
r_scbond_it	4.705
r_mcbond_it	4.114
r_angle_refined_deg	1.33
r_angle_other_deg	0.98
r_chiral_restr	0.09
r_bond_refined_d	0.011
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2434
Nucleic Acid Atoms
Solvent Atoms	8
Heterogen Atoms	21

Software

Software
Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling