3HRB

p38 kinase Crystal structure in complex with small molecule inhibitor


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1A9UPDB ENTRY 1A9U

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.529822% PEG 3350, 0.2M NaCl, 0.1M Bis-Tris pH 6.5, 1mM THP, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.9157.73

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 45.22α = 90
b = 86.75β = 90
c = 122.23γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU2005-06-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF1.54180

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym I (Observed)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
12.270.74484.20.0570.0579.51.9404192080635.9
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
2.22.3289.10.3670.3672.21.85586

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1A9U2.229.74041919725107282.580.2170.2140.26RANDOM26.83
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]
-0.44-0.771.2
RMS Deviations
KeyRefinement Restraint Deviation
p_scangle_it2.402
p_scbond_it1.441
p_mcangle_it1.333
p_angle_d1.202
p_mcbond_it0.718
p_chiral_restr0.071
p_bond_d0.01
p_plane_restr0.005
p_angle_deg
p_planar_d
RMS Deviations
KeyRefinement Restraint Deviation
p_scangle_it2.402
p_scbond_it1.441
p_mcangle_it1.333
p_angle_d1.202
p_mcbond_it0.718
p_chiral_restr0.071
p_bond_d0.01
p_plane_restr0.005
p_angle_deg
p_planar_d
p_hb_or_metal_coord
p_singtor_nbd
p_multtor_nbd
p_xhyhbond_nbd
p_xyhbond_nbd
p_planar_tor
p_staggered_tor
p_orthonormal_tor
p_transverse_tor
p_special_tor
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2766
Nucleic Acid Atoms
Solvent Atoms180
Heterogen Atoms25

Software

Software
Software NamePurpose
SCALAdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction