5R8X | pdb_00005r8x

PanDDA analysis group deposition Form1 MAP kinase p38-alpha -- Fragment N11396a in complex with MAP kinase p38-alpha

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.9	291	27.5% PEG3350, 0.1 M Bis-Tris propane, pH 6.9, 50 mM ammonium sulfate, 0.2 M 1:1 magnesium chloride:magnesium sulfate, 10% glycerol

Crystal Properties
Matthews coefficient	Solvent content
3.07	59.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 45.91	α = 90
b = 86.614	β = 90
c = 127.537	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	PIXEL	DECTRIS PILATUS 6M		2016-02-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.92819	Diamond	I04-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	1.73	127.54	98.8	0.113	0.123	0.049	0.991	7.1	6.5		53273

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.73	1.77	98.9		1.517	1.649	0.638	0.485		6.5	3898

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 (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	THROUGHOUT	PDB entry 6SO1	1.73	71.65	49378	2578	96.2	0.2206	0.2191	0.24	0.2486	0.26	RANDOM	26.922

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]
0.45			-0.36		-0.09

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.735
r_dihedral_angle_4_deg	17.249
r_dihedral_angle_3_deg	16.354
r_dihedral_angle_1_deg	6.775
r_mcangle_it	3.615
r_mcbond_other	1.956
r_mcbond_it	1.941
r_angle_refined_deg	1.537
r_angle_other_deg	1.529
r_chiral_restr	0.07

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.735
r_dihedral_angle_4_deg	17.249
r_dihedral_angle_3_deg	16.354
r_dihedral_angle_1_deg	6.775
r_mcangle_it	3.615
r_mcbond_other	1.956
r_mcbond_it	1.941
r_angle_refined_deg	1.537
r_angle_other_deg	1.529
r_chiral_restr	0.07
r_bond_other_d	0.016
r_bond_refined_d	0.009
r_gen_planes_refined	0.008
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2746
Nucleic Acid Atoms
Solvent Atoms	255
Heterogen Atoms	30

Software

Software
Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
REFMAC	phasing

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.