6YKD

Human Pim-1 kinase in complex with an inhibitor identified by virtual screening

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	COUNTER-DIFFUSION	6.3	277	0.1 M imidazole pH 6.3 1 M sodium acetate

Crystal Properties
Matthews coefficient	Solvent content
3.02	59.25

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 98.645	α = 90
b = 98.645	β = 90
c = 80.699	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	PIXEL	DECTRIS PILATUS 6M		2015-02-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID29	0.9762	ESRF	ID29

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	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	1.86	19.61	98.3	0.065	0.071	0.026	0.996	14.9	6.7		36740

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.862	1.894	99.8		0.585	0.638	0.248	0.853	2.2	6

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	3R04	1.86	19.61	34889	1851	98.12	0.1602	0.1584	0.1942	RANDOM	43.51

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]
0.71	0.36		0.71		-2.31

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.185
r_dihedral_angle_4_deg	21.841
r_dihedral_angle_3_deg	13.757
r_dihedral_angle_1_deg	6.556
r_angle_refined_deg	1.734
r_angle_other_deg	1.454
r_chiral_restr	0.088
r_bond_refined_d	0.013
r_gen_planes_refined	0.01
r_gen_planes_other	0.002

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.185
r_dihedral_angle_4_deg	21.841
r_dihedral_angle_3_deg	13.757
r_dihedral_angle_1_deg	6.556
r_angle_refined_deg	1.734
r_angle_other_deg	1.454
r_chiral_restr	0.088
r_bond_refined_d	0.013
r_gen_planes_refined	0.01
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2268
Nucleic Acid Atoms
Solvent Atoms	200
Heterogen Atoms	45

Software

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

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.