3QF9 | pdb_00003qf9

Crystal structure of human proto-oncogene serine threonine kinase (PIM1) in complex with a consensus peptide and a furan-thiazolidinedione ligand

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2C3I	pdb entry 2C3I

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	277	0.1 M BTP, 20 % PEG 3350 10 % ethylene glycol, VAPOR DIFFUSION, SITTING DROP, temperature 277K, pH 6.5

Crystal Properties
Matthews coefficient	Solvent content
2.99	58.85

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 97.843	α = 90
b = 97.843	β = 90
c = 80.428	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	IMAGE PLATE	RIGAKU RAXIS HTC		2009-03-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-E SUPERBRIGHT	1.5

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	2.2	37.484	100	0.101	0.101	13.3	5.6	22340	22340			39.9

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.2	2.32	100		0.851	0.851	0.9	5.5	3251

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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 2C3I	2.2	37.48	22314	22310	1110	99.98	0.1878	0.1878	0.1858	0.18	0.2268	0.22	RANDOM	40.7836

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]
0.92	0.46		0.92		-1.39

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.699
r_dihedral_angle_4_deg	15.974
r_dihedral_angle_3_deg	14.62
r_scangle_it	9.961
r_scbond_it	8.489
r_dihedral_angle_1_deg	6.102
r_mcangle_it	5.243
r_mcbond_it	3.586
r_angle_refined_deg	1.569
r_mcbond_other	1.165

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.699
r_dihedral_angle_4_deg	15.974
r_dihedral_angle_3_deg	14.62
r_scangle_it	9.961
r_scbond_it	8.489
r_dihedral_angle_1_deg	6.102
r_mcangle_it	5.243
r_mcbond_it	3.586
r_angle_refined_deg	1.569
r_mcbond_other	1.165
r_angle_other_deg	0.938
r_chiral_restr	0.097
r_bond_refined_d	0.016
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2270
Nucleic Acid Atoms
Solvent Atoms	131
Heterogen Atoms	28

Software

Software
Software Name	Purpose
SCALA	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
CrystalClear	data collection
MOSFLM	data reduction

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.