5XJB | pdb_00005xjb

The Crystal Structure of the Minimal Core Domain of the Microtubule Depolymerizer KIF2C Complexed with ADP-Mg-BeFx

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1V8K

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		297	potassium sodium tartrate tetrahydrate, MES, pH 6.0

Crystal Properties
Matthews coefficient	Solvent content
2.9	57.62

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 89.452	α = 90
b = 166.593	β = 90
c = 75.5	γ = 90

Symmetry
Space Group	P 21 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	98	PIXEL	DECTRIS PILATUS3 S 6M		2017-02-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-17A	0.98	Photon Factory	BL-17A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	3.1	30	99.9	0.07	0.029	23.2	6.5		21151

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3.1	3.18	100		0.639	0.23	2.5	6.5

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	1V8K	3.1	30	20045	1061	99.78	0.2042	0.2012	0.21	0.2614	0.26	RANDOM	79.629

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]
10.25			-6.08		-4.17

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.541
r_dihedral_angle_4_deg	18.764
r_dihedral_angle_3_deg	16.921
r_dihedral_angle_1_deg	9.931
r_angle_refined_deg	1.694
r_angle_other_deg	1.27
r_chiral_restr	0.087
r_bond_refined_d	0.013
r_gen_planes_refined	0.007
r_bond_other_d	0.006

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.541
r_dihedral_angle_4_deg	18.764
r_dihedral_angle_3_deg	16.921
r_dihedral_angle_1_deg	9.931
r_angle_refined_deg	1.694
r_angle_other_deg	1.27
r_chiral_restr	0.087
r_bond_refined_d	0.013
r_gen_planes_refined	0.007
r_bond_other_d	0.006
r_gen_planes_other	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5275
Nucleic Acid Atoms
Solvent Atoms	5
Heterogen Atoms	64

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	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.