3HP5 | pdb_00003hp5

Crystal Structure of Human p38alpha complexed with a pyrimidopyridazinone 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
2.23	44.92

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 65.045	α = 90
b = 74.022	β = 90
c = 76.697	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	MAR CCD 165 mm		2001-08-15	M	SINGLE WAVELENGTH

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

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	2.3	40	92.7	0.062	0.062	21.35	3.7	15856	15856	-1.5	-3	48.4

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	2.3	2.38	63.6		0.449	0.449	2.1	3	1066

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 (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	FOURIER SYNTHESIS	THROUGHOUT	2.3	37.01	15033	780	92.81	0.21666	0.21666	0.21431	0.21	0.26185	0.26	RANDOM	35.879

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]
-1.55			-1.47		3.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.674
r_dihedral_angle_4_deg	19.455
r_dihedral_angle_3_deg	17.393
r_dihedral_angle_1_deg	5.884
r_scangle_it	1.538
r_angle_refined_deg	1.279
r_scbond_it	1.055
r_angle_other_deg	0.885
r_mcangle_it	0.715
r_mcbond_it	0.633
r_symmetry_vdw_other	0.223
r_nbd_refined	0.202
r_nbd_other	0.19
r_nbtor_refined	0.184
r_symmetry_hbond_refined	0.166
r_xyhbond_nbd_refined	0.158
r_symmetry_vdw_refined	0.134
r_nbtor_other	0.088
r_mcbond_other	0.078
r_chiral_restr	0.07
r_bond_refined_d	0.009
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	2665
Nucleic Acid Atoms
Solvent Atoms	166
Heterogen Atoms	66

Software

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