9MHB | pdb_00009mhb

Crystal Structure of Human P38 alpha MAPK In Complex with MW01-14-064SRM

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4F9Y

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	292	Protein: 20.0 mg/ml, 0.15M Sodium chloride, 0.02M Tris-HCl (pH 8.3), 1mM TCEP; Screen: 0.15M Ammomium acetate, 0.1M Bis-Tris (pH 5.5), 16% (w/v) PEG1000; Soak: 3 hrs, 5mM ligand in screen solution; Cryo: 10% Glycerol in screen solution.

Crystal Properties
Matthews coefficient	Solvent content
2.4	48.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 66.446	α = 90
b = 74.862	β = 90
c = 78.065	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		2011-10-10	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	1.65	30	100	0.044	0.044	0.048	0.018	0.997	44.9	7.4		47571		-3	26

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.65	1.68	100		0.969	0.969	0.381	0.746	2.3	7.4

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	1.65	28.3	45229	2273	99.92	0.17393	0.17254	0.1832	0.20174	0.2072	RANDOM	31.536

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]
0.2			-0.52		0.33

RMS Deviations
Key	Refinement Restraint Deviation
r_long_range_B_refined	8.093
r_long_range_B_other	8.009
r_dihedral_angle_3_deg	7.391
r_scangle_other	4.806
r_dihedral_angle_2_deg	4.462
r_mcangle_it	3.177
r_mcangle_other	3.176
r_scbond_it	3.131
r_scbond_other	3.13
r_dihedral_angle_1_deg	3.033
r_mcbond_it	2.085
r_mcbond_other	2.051
r_angle_refined_deg	1.524
r_angle_other_deg	0.519
r_chiral_restr	0.08
r_gen_planes_refined	0.017
r_gen_planes_other	0.013
r_bond_refined_d	0.005
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	2724
Nucleic Acid Atoms
Solvent Atoms	323
Heterogen Atoms	84

Software

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