3OBG | pdb_00003obg

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

X-RAY DIFFRACTION

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	10-15% PEG 4000, 0.1M Cacodylic acid, 50 mM n-octyl-beta-D-glucoside, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.24	45.13

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 65.118	α = 90
b = 73.697	β = 90
c = 77.08	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	2.8	30.25	99.1	0.143	0.109	11.3			9563	1	1

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.8	3.02	99.8		2.2		1847

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	2.8	30.25	8733	712	98.52	0.22216	0.21398	0.22	0.32284	RANDOM	37.858

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]
0.46			-2.72		2.26

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.685
r_dihedral_angle_4_deg	26.898
r_dihedral_angle_3_deg	23.541
r_dihedral_angle_1_deg	9.066
r_scangle_it	3.824
r_scbond_it	2.385
r_angle_refined_deg	2.246
r_mcangle_it	1.742
r_mcbond_it	1.01
r_nbtor_refined	0.341

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.685
r_dihedral_angle_4_deg	26.898
r_dihedral_angle_3_deg	23.541
r_dihedral_angle_1_deg	9.066
r_scangle_it	3.824
r_scbond_it	2.385
r_angle_refined_deg	2.246
r_mcangle_it	1.742
r_mcbond_it	1.01
r_nbtor_refined	0.341
r_nbd_refined	0.286
r_symmetry_vdw_refined	0.259
r_xyhbond_nbd_refined	0.194
r_chiral_restr	0.133
r_symmetry_hbond_refined	0.124
r_bond_refined_d	0.023
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2675
Nucleic Acid Atoms
Solvent Atoms	25
Heterogen Atoms	27

Software

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.