5RA0

PanDDA analysis group deposition Form1 MAP kinase p38-alpha -- Fragment N13421a in complex with MAP kinase p38-alpha


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.929127.5% 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 coefficientSolvent content
3.0559.73

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 45.95α = 90
b = 87.04β = 90
c = 126.29γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2016-02-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-10.92819DiamondI04-1

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)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.9163.1499.80.2050.2260.0930.98711.46.240131
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)RedundancyNumber Unique Reflections (All)
11.911.961001.4551.5780.6040.5816.82903

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONFOURIER SYNTHESISTHROUGHOUTPDB entry 6SO11.9163.2238072199799.730.22070.21880.2571RANDOM33.338
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]
-1.492.24-0.75
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.839
r_dihedral_angle_4_deg16.754
r_dihedral_angle_3_deg16.242
r_dihedral_angle_1_deg6.901
r_mcangle_it4.817
r_angle_other_deg3.053
r_mcbond_other2.876
r_mcbond_it2.846
r_angle_refined_deg1.642
r_chiral_restr0.078
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.839
r_dihedral_angle_4_deg16.754
r_dihedral_angle_3_deg16.242
r_dihedral_angle_1_deg6.901
r_mcangle_it4.817
r_angle_other_deg3.053
r_mcbond_other2.876
r_mcbond_it2.846
r_angle_refined_deg1.642
r_chiral_restr0.078
r_bond_other_d0.036
r_gen_planes_other0.017
r_bond_refined_d0.014
r_gen_planes_refined0.009
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2726
Nucleic Acid Atoms
Solvent Atoms231
Heterogen Atoms31

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
REFMACphasing