9Q5B | pdb_00009q5b

Crystal Structure of Human P38 alpha MAPK in Complex with MW01-21-114SRM

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4EWQ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	293	Protein: 9.2 mg/ml, 0.15M Sodium chloride, 0.02M Tris-HCl (pH 8.3), 1mM TCEP; Screen: 0.1M Ammomium acetate, 0.1M Bis-Tris (pH 5.5), 17% (w/v) PEG10000, 2mM 4FPP (4-[3-(4-fluorophenyl)-1H-pyrazol-4-yl]pyridine); Soak: 24 hrs, 5mM ligand (MW01-25-195SRM) in screen solution; Cryo: 0.1M Bis-Tris (pH 5.5), 20% (w/v) PEG10000

Crystal Properties
Matthews coefficient	Solvent content
2.4	48.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 66.074	α = 90
b = 74.8	β = 90
c = 78.662	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	100	CCD	MARMOSAIC 300 mm CCD		2025-07-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-G	0.97856	APS	21-ID-G

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	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	30	100	0.067	0.067	0.072	0.026	0.998	33.2	7.8		25632		-3	38.5

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.05	2.09	100		0.473	0.723	1.8	8.2

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	MOLECULAR REPLACEMENT	THROUGHOUT	2.05	28.21	23700	1274	99.52	0.1934	0.19099	0.2017	0.23604	0.2385	RANDOM	50.663

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]
2.98			-1.25		-1.72

RMS Deviations
Key	Refinement Restraint Deviation
r_long_range_B_refined	10.982
r_long_range_B_other	10.966
r_scangle_other	8.421
r_dihedral_angle_3_deg	8.103
r_scbond_it	6.095
r_scbond_other	6.093
r_mcangle_it	6.033
r_mcangle_other	6.032
r_mcbond_it	4.514
r_mcbond_other	4.512
r_dihedral_angle_2_deg	2.885
r_dihedral_angle_1_deg	2.794
r_angle_refined_deg	1.725
r_angle_other_deg	0.552
r_chiral_restr	0.089
r_gen_planes_refined	0.02
r_gen_planes_other	0.016
r_bond_refined_d	0.007
r_bond_other_d	0.001
r_dihedral_angle_4_deg
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2693
Nucleic Acid Atoms
Solvent Atoms	155
Heterogen Atoms	42

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
HKL-3000	data scaling
REFMAC	phasing