3O8P | pdb_00003o8p

Conformational plasticity of p38 MAP kinase DFG motif mutants in response to inhibitor binding

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1ZYJ	PDB entry 1ZYJ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6	295	10-20% PEG4000, 0.1M cacodylic acid, 50mM n-octyl-beta-D-glucoside, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.26	45.51

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 65.931	α = 90
b = 73.587	β = 90
c = 76.828	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	93	CCD	ADSC QUANTUM 4	Mirrors		M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X4A	0.98	NSLS	X4A

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	2.1	34.05	99.8	0.085	0.063	21			22492		1

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)
	2.1	2.18	99.2		0.046	0.042	4.1	6.1	2173

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 Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 1ZYJ	2.1	34.05	20631	1738	99.62	0.21815	0.21328	0.2148	0.27582	RANDOM	28.246

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]
-0.96			-0.76		1.72

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.644
r_dihedral_angle_4_deg	21.54
r_dihedral_angle_3_deg	18.779
r_dihedral_angle_1_deg	6.44
r_scangle_it	2.733
r_scbond_it	1.757
r_angle_refined_deg	1.586
r_mcangle_it	1.385
r_mcbond_it	0.782
r_nbtor_refined	0.309
r_symmetry_vdw_refined	0.276
r_nbd_refined	0.225
r_symmetry_hbond_refined	0.2
r_xyhbond_nbd_refined	0.153
r_chiral_restr	0.119
r_bond_refined_d	0.011
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2698
Nucleic Acid Atoms
Solvent Atoms	287
Heterogen Atoms	45

Software

Software
Software Name	Purpose
ADSC	data collection
AMoRE	phasing
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling