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Crystal structure of a pyrrolopyridine inhibitor bound to MAPKAP Kinase-2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other Structure of MAPKAP Kinase-2/AMP-PNP complex solved using ERK-2 as a starting model for molecular replacement
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.4 298 Protein 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 coefficient Solvent content 4.5 72.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 253.941 α = 90 b = 253.941 β = 90 c = 253.941 γ = 90
Symmetry Space Group F 41 3 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 210 2005-07-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 17-ID 1.0 APS 17-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) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 3.7 20 99.5 0.051 0.051 11.6 7.4 7892 7853 -1 105
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) Redundancy Number Unique Reflections (All) 3.7 3.83 99.5 0.407 0.407 3.8 6.9 752
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT Structure of MAPKAP Kinase-2/AMP-PNP complex solved using ERK-2 as a starting model for molecular replacement 3.8 20 8020 7247 335 99.52 0.303 0.3 0.2789 0.374 0.3477 RANDOM 135.676
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 Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.3 r_dihedral_angle_3_deg 22.36 r_dihedral_angle_4_deg 15.832 r_dihedral_angle_1_deg 7.15 r_scangle_it 1.632 r_angle_refined_deg 1.443 r_mcangle_it 1.331 r_scbond_it 0.907 r_mcbond_it 0.739 r_nbtor_refined 0.332
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.3 r_dihedral_angle_3_deg 22.36 r_dihedral_angle_4_deg 15.832 r_dihedral_angle_1_deg 7.15 r_scangle_it 1.632 r_angle_refined_deg 1.443 r_mcangle_it 1.331 r_scbond_it 0.907 r_mcbond_it 0.739 r_nbtor_refined 0.332 r_nbd_refined 0.264 r_symmetry_vdw_refined 0.204 r_xyhbond_nbd_refined 0.198 r_symmetry_hbond_refined 0.159 r_chiral_restr 0.092 r_bond_refined_d 0.012 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2298 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 23
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction ADSC data collection HKL-2000 data reduction X-PLOR phasing