5IPJ

Crystal structure of human Pim-1 kinase in complex with a quinazolinone-pyrrolopyrrolone 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
3.34	63.19

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 97.408	α = 90
b = 97.408	β = 90
c = 80.663	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	RIGAKU SATURN 92	VariMax HF	2012-10-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-E SUPERBRIGHT	1.5418

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	98.2	0.079	12.9	4.2		25440

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	97.3		0.44	3.3	4.1

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	28.12	23693	1269	98.23	0.18135	0.17926	0.22114	RANDOM	42.691

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]
-0.07	-0.04		-0.07		0.23

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.023
r_dihedral_angle_4_deg	13.045
r_dihedral_angle_3_deg	12.958
r_dihedral_angle_1_deg	4.958
r_long_range_B_refined	4.647
r_long_range_B_other	4.477
r_scangle_other	2.72
r_mcangle_it	2.556
r_mcangle_other	2.555
r_scbond_it	1.611
r_scbond_other	1.61
r_mcbond_other	1.591
r_mcbond_it	1.59
r_angle_refined_deg	1.053
r_angle_other_deg	0.709
r_chiral_restr	0.062
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	164
Heterogen Atoms	45

Software

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