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Crystal structure of a benzthiophene lead bound to MAPKAP Kinase-2 (MK-2)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1A06 1A06,1ATP,1CDK,2PHK experimental model PDB 1ATP 1A06,1ATP,1CDK,2PHK experimental model PDB 1CDK 1A06,1ATP,1CDK,2PHK experimental model PDB 2PHK 1A06,1ATP,1CDK,2PHK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.4 298 MK-2 protein at 5 mg/ml equilibrated against a well solution of 1.6 - 2.0 M Sodium malonate at pH 5.4, vapor diffusion, hanging drop, temperature 298K
Crystal Properties Matthews coefficient Solvent content 4.54 72.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 254.598 α = 90 b = 254.598 β = 90 c = 254.598 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 2005-03-02 SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 17-ID 1.00 APS 17-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 3.5 30 93.2 0.083 19.778 7.5 8772
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 3.5 3.62 95.1 0.352 6.9 860
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 MOLECULAR REPLACEMENT THROUGHOUT 1A06,1ATP,1CDK,2PHK 3.5 30 8772 424 93.07 0.267 0.265 0.2623 0.296 0.2879 RANDOM 98.046
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 39.322 r_dihedral_angle_3_deg 21.834 r_dihedral_angle_4_deg 21.426 r_dihedral_angle_1_deg 5.992 r_scangle_it 1.758 r_angle_refined_deg 1.397 r_mcangle_it 1.203 r_scbond_it 0.957 r_mcbond_it 0.652 r_chiral_restr 0.078
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.322 r_dihedral_angle_3_deg 21.834 r_dihedral_angle_4_deg 21.426 r_dihedral_angle_1_deg 5.992 r_scangle_it 1.758 r_angle_refined_deg 1.397 r_mcangle_it 1.203 r_scbond_it 0.957 r_mcbond_it 0.652 r_chiral_restr 0.078 r_bond_refined_d 0.01 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2298 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 19
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction ADSC data collection HKL-2000 data reduction AMoRE phasing