5R9P

PanDDA analysis group deposition Form1 MAP kinase p38-alpha -- Fragment N13430a 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
3.0459.53

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 45.951α = 90
b = 86.183β = 90
c = 126.899γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2015-12-11MSINGLE 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
11.7229.7799.30.0470.0510.02121.66.654172
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)
11.721.7697.50.7870.8540.3280.7586.53908

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 6SO11.7229.7951425268499.090.17470.17360.1954RANDOM30.994
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]
-0.340.46-0.12
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.232
r_dihedral_angle_4_deg20.384
r_dihedral_angle_3_deg15.748
r_dihedral_angle_1_deg6.508
r_mcangle_it4.492
r_mcbond_other2.831
r_mcbond_it2.818
r_angle_other_deg1.7
r_angle_refined_deg1.626
r_chiral_restr0.081
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.232
r_dihedral_angle_4_deg20.384
r_dihedral_angle_3_deg15.748
r_dihedral_angle_1_deg6.508
r_mcangle_it4.492
r_mcbond_other2.831
r_mcbond_it2.818
r_angle_other_deg1.7
r_angle_refined_deg1.626
r_chiral_restr0.081
r_bond_refined_d0.01
r_gen_planes_refined0.009
r_bond_other_d0.004
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2746
Nucleic Acid Atoms
Solvent Atoms265
Heterogen Atoms32

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
REFMACphasing