1XWS | pdb_00001xws

Crystal Structure of the human PIM1 kinase domain

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	277	Na2SO4, Bis-Tris propane, PEG3350, Ethylene Glycol, DMSO, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
3.7	66.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 99.55	α = 90
b = 99.55	β = 90
c = 80.06	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	Multi-layer VariMax HR	2004-10-21	M	SINGLE WAVELENGTH

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

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	1.8	86.07	99.5	0.068	0.068	18.4	6.3	41697	41578			30.1

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)
1	1.8	1.9	98.2		0.781	0.781	1.5	4.1	5939

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	1.8	58.67	47251	39589	2136	58.67	0.18164	0.18164	0.17999	0.18	0.21336	0.21	RANDOM	36.881

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]
0.01	0.01		0.01		-0.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.6
r_dihedral_angle_4_deg	18.091
r_dihedral_angle_3_deg	13.182
r_dihedral_angle_1_deg	5.769
r_scangle_it	4.094
r_scbond_it	2.586
r_angle_refined_deg	1.914
r_mcangle_it	1.648
r_mcbond_it	1.026
r_nbtor_refined	0.306
r_nbd_refined	0.201
r_symmetry_hbond_refined	0.173
r_xyhbond_nbd_refined	0.16
r_chiral_restr	0.112
r_symmetry_vdw_refined	0.108
r_bond_refined_d	0.018
r_gen_planes_refined	0.007
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2213
Nucleic Acid Atoms
Solvent Atoms	242
Heterogen Atoms	36

Software

Software
Software Name	Purpose
REFMAC	refinement
CrystalClear	data reduction
CrystalClear	data scaling
PHASER	phasing