5R8W

PanDDA analysis group deposition Form1 MAP kinase p38-alpha -- Fragment K00283c 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 = 45.78α = 90
b = 86.1β = 90
c = 127.51γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2016-02-10MSINGLE 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
11.571.3699.60.0480.0520.020.99917.66.581204
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)
11.51.5499.51.1961.3240.5590.4855.55921

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 6SO11.571.3677103402499.450.18610.18530.2011RANDOM26.915
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]
0.19-0.250.06
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.201
r_dihedral_angle_4_deg19.961
r_dihedral_angle_3_deg15.473
r_dihedral_angle_1_deg6.138
r_mcangle_it3.953
r_mcbond_other2.315
r_mcbond_it2.287
r_angle_other_deg1.71
r_angle_refined_deg1.672
r_chiral_restr0.082
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.201
r_dihedral_angle_4_deg19.961
r_dihedral_angle_3_deg15.473
r_dihedral_angle_1_deg6.138
r_mcangle_it3.953
r_mcbond_other2.315
r_mcbond_it2.287
r_angle_other_deg1.71
r_angle_refined_deg1.672
r_chiral_restr0.082
r_bond_refined_d0.011
r_gen_planes_refined0.01
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 Atoms242
Heterogen Atoms27

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
REFMACphasing