2OBJ | pdb_00002obj

Crystal structure of human PIM-1 Kinase in complex with inhibitor

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1XQZ	pdb entry 1XQZ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5	296	1M ammonium phosphate (dibasic), 300mM NaCl, 100mM citrate buffer, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 296K

Crystal Properties
Matthews coefficient	Solvent content
2.9	57.65

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 97.264	α = 90
b = 97.264	β = 90
c = 80.827	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 IV		2005-12-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU300

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.4	500	98.6	0.077	12.8	8.1	17157	16917		-1

Refinement

Statistics
Diffraction ID	Structure Solution Method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Work (Depositor)	R-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	pdb entry 1XQZ	2.5	500	15146	14369	1436		0.205	0.246	random

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]

RMS Deviations
Key	Refinement Restraint Deviation
c_angle_d	1.204
c_bond_d	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2228
Nucleic Acid Atoms
Solvent Atoms	68
Heterogen Atoms	23

Software

Software
Software Name	Purpose
CrystalClear	data collection
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
CNS	phasing