5RA8 | pdb_00005ra8

PanDDA analysis group deposition Form1 MAP kinase p38-alpha -- Fragment N05711b 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
3.04	59.56

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 45.887	α = 90
b = 86.638	β = 90
c = 126.501	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		2016-02-12	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	1.78	29.71	99.4	0.075	0.082	0.032	0.999	15.3	6.5		48854

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	1.78	1.83	94		0.893	0.974	0.382	0.684		6.2	3358

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	1.78	29.73	46365	2427	99.38	0.1832	0.1818	0.2	0.2101	0.22	RANDOM	29.371

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]
-0.5			0.06		0.44

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.283
r_dihedral_angle_4_deg	22.824
r_dihedral_angle_3_deg	15.339
r_dihedral_angle_1_deg	6.578
r_mcangle_it	3.774
r_angle_other_deg	2.922
r_mcbond_other	2.286
r_mcbond_it	2.264
r_angle_refined_deg	1.544
r_chiral_restr	0.07

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.283
r_dihedral_angle_4_deg	22.824
r_dihedral_angle_3_deg	15.339
r_dihedral_angle_1_deg	6.578
r_mcangle_it	3.774
r_angle_other_deg	2.922
r_mcbond_other	2.286
r_mcbond_it	2.264
r_angle_refined_deg	1.544
r_chiral_restr	0.07
r_bond_other_d	0.036
r_gen_planes_other	0.015
r_gen_planes_refined	0.009
r_bond_refined_d	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2732
Nucleic Acid Atoms
Solvent Atoms	255
Heterogen Atoms	34

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.