3HP2 | pdb_00003hp2

Crystal Structure of Human p38alpha complexed with a pyridinone compound

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	9	298	20-30% PEG3000, 10 mM CaCl2, 50 mM CHES, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

Crystal Properties
Matthews coefficient	Solvent content
2.27	45.78

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 65.246	α = 90
b = 74.44	β = 90
c = 77.238	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	110	CCD	ADSC QUANTUM 210	crystal monochromator	2001-10-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 17-ID	1.0	APS	17-ID

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	2.15	50	100	0.07	0.07	29.1	5.2	21118	21118	-1.5	-3	44.2

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	2.15	2.23	98.1		0.307	0.307	3	5.2	2013

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	2.15	23.38	20003	1067	99.63	0.20792	0.20566	0.2	0.25189	0.25	RANDOM	34.235

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]
-0.85			-0.8		1.66

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.367
r_dihedral_angle_4_deg	17.504
r_dihedral_angle_3_deg	16.828
r_dihedral_angle_1_deg	6.449
r_scangle_it	2.142
r_scbond_it	1.481
r_angle_refined_deg	1.309
r_mcangle_it	1.145
r_angle_other_deg	0.899
r_mcbond_it	0.714
r_symmetry_vdw_other	0.253
r_symmetry_vdw_refined	0.213
r_nbd_refined	0.207
r_nbd_other	0.188
r_nbtor_refined	0.184
r_xyhbond_nbd_refined	0.152
r_symmetry_hbond_refined	0.149
r_mcbond_other	0.119
r_nbtor_other	0.089
r_chiral_restr	0.076
r_bond_refined_d	0.01
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2746
Nucleic Acid Atoms
Solvent Atoms	211
Heterogen Atoms	60

Software

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