3GC9 | pdb_00003gc9

The structure of p38beta C119S, C162S in complex with a dihydroquinazolinone inhibitor

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3GC8

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.4	291	12-14% PEG 3350, 0.12 M ammonium fluoride, 1% DMSO, 30 uM CTAB, 10-20 mM LiCl, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.25	45.39

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 39.184	α = 90
b = 158.823	β = 91.59
c = 60.874	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	MAR CCD 165 mm		2002-12-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 17-BM	1.00	APS	17-BM

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	2.05	50	98.5	0.058	8.8	5.3	46456	45759		-3	32.7

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.05	2.12	92		0.263	1.6	3.5	4583

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	THROUGHOUT	3GC8	2.05	30	43404	2309	98.52	0.22443	0.22173	0.22	0.27531	0.27	RANDOM	33.395

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]
0.13		0.06	-0.78		0.65

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.453
r_dihedral_angle_4_deg	17.75
r_dihedral_angle_3_deg	15.743
r_dihedral_angle_1_deg	5.735
r_scangle_it	2.49
r_scbond_it	1.574
r_angle_refined_deg	1.315
r_mcangle_it	1.121
r_mcbond_it	0.623
r_nbtor_refined	0.301
r_symmetry_vdw_refined	0.274
r_nbd_refined	0.201
r_xyhbond_nbd_refined	0.167
r_symmetry_hbond_refined	0.145
r_symmetry_metal_ion_refined	0.136
r_chiral_restr	0.09
r_metal_ion_refined	0.085
r_bond_refined_d	0.011
r_gen_planes_refined	0.004
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_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_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	5384
Nucleic Acid Atoms
Solvent Atoms	346
Heterogen Atoms	75

Software

Software
Software Name	Purpose
REFMAC	refinement
CNS	refinement
MAR345dtb	data collection
HKL-2000	data reduction
HKL-2000	data scaling
CNS	phasing