3HEC | pdb_00003hec

P38 in complex with Imatinib

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1ZYJ	PDB ENTRY 1ZYJ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6	295	10-20% PEG 4000, 0.1 M Cacodylic acid, 50 mM n-octyl-beta-D-glucoside, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.25	45.25

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 65.029	α = 90
b = 74.031	β = 90
c = 74.497	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	93	CCD	ADSC QUANTUM 4	Mirrors	2007-06-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X4A	0.98	NSLS	X4A

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	2.4	40	97	0.77	0.55	19.9			14641

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)
	2.4	2.49	100		0.513	0.438	3		1428

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	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 1ZYJ	2.5	40	1	12297	642	99.88	0.22226	0.21811	0.2172	0.30014	0.293	RANDOM	39.267

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]
-0.04			1.31		-1.27

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.795
r_dihedral_angle_4_deg	22.727
r_dihedral_angle_3_deg	21.485
r_dihedral_angle_1_deg	7.626
r_scangle_it	3.395
r_scbond_it	2.162
r_angle_refined_deg	1.912
r_mcangle_it	1.652
r_mcbond_it	0.917
r_nbtor_refined	0.323
r_symmetry_vdw_refined	0.264
r_nbd_refined	0.249
r_xyhbond_nbd_refined	0.242
r_symmetry_hbond_refined	0.202
r_chiral_restr	0.154
r_bond_refined_d	0.018
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2668
Nucleic Acid Atoms
Solvent Atoms	89
Heterogen Atoms	57

Software

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