2P3G

Crystal structure of a pyrrolopyridine inhibitor bound to MAPKAP Kinase-2


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelOtherStructure of MAPKAP Kinase-2/AMP-PNP complex solved using ERK-2 as a starting model for molecular replacement

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.4298Protein solution (5 mg/ml) euqilibrated against 1.6 - 2.0 M sodium malonate at pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal Properties
Matthews coefficientSolvent content
4.572.66

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 253.941α = 90
b = 253.941β = 90
c = 253.941γ = 90
Symmetry
Space GroupF 41 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2102005-07-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 17-ID1.0APS17-ID

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
13.72099.50.0510.05111.67.478927853-1105
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)
3.73.8399.50.4070.4073.86.9752

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 DIFFRACTIONFOURIER SYNTHESISTHROUGHOUTStructure of MAPKAP Kinase-2/AMP-PNP complex solved using ERK-2 as a starting model for molecular replacement3.8208020724733599.520.3030.30.374RANDOM135.676
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.3
r_dihedral_angle_3_deg22.36
r_dihedral_angle_4_deg15.832
r_dihedral_angle_1_deg7.15
r_scangle_it1.632
r_angle_refined_deg1.443
r_mcangle_it1.331
r_scbond_it0.907
r_mcbond_it0.739
r_nbtor_refined0.332
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.3
r_dihedral_angle_3_deg22.36
r_dihedral_angle_4_deg15.832
r_dihedral_angle_1_deg7.15
r_scangle_it1.632
r_angle_refined_deg1.443
r_mcangle_it1.331
r_scbond_it0.907
r_mcbond_it0.739
r_nbtor_refined0.332
r_nbd_refined0.264
r_symmetry_vdw_refined0.204
r_xyhbond_nbd_refined0.198
r_symmetry_hbond_refined0.159
r_chiral_restr0.092
r_bond_refined_d0.012
r_gen_planes_refined0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2298
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms23

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
HKL-2000data reduction
X-PLORphasing