5KZI

Crystal structure of human Pim-1 kinase in complex with an imidazopyridazine inhibitor.

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	277	1.0M LiCl, 0.1M TRIS pH8.0, 20% PEG6K

Crystal Properties
Matthews coefficient	Solvent content
3.27	62.37

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 95.998	α = 90
b = 95.998	β = 90
c = 81.251	γ = 120

Symmetry
Space Group	P 65

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		2016-01-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.1	0.977408	ALS	5.0.1

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	2.1	30	100	0.121	7.6	9.5		24982

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	2.1	2.18	100		0.535	4.75	9.5

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2.1	30	23667	1236	99.95	0.1795	0.17813	0.20469	RANDOM	39.058

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]
0.19	0.1		0.19		-0.62

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.131
r_dihedral_angle_4_deg	13.614
r_dihedral_angle_3_deg	12.51
r_long_range_B_refined	5.249
r_dihedral_angle_1_deg	5.188
r_long_range_B_other	5.032
r_scangle_other	3.087
r_mcangle_it	2.65
r_mcangle_other	2.649
r_scbond_it	1.793
r_scbond_other	1.793
r_mcbond_it	1.607
r_mcbond_other	1.605
r_angle_refined_deg	1.055
r_angle_other_deg	0.696
r_chiral_restr	0.061
r_bond_refined_d	0.006
r_gen_planes_refined	0.004
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2225
Nucleic Acid Atoms
Solvent Atoms	170
Heterogen Atoms	31

Software

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