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Structure of Human Myotonic Dystrophy Protein Kinase in Complex with the Bisindoylmaleide inhibitor BIM VIII
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2ESM PDB ENTRY 2ESM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7 1M AMMONIUM SULPHATE, 1.5% PEG 3350, 0.1M BIS-TRIS PH7.0
Crystal Properties Matthews coefficient Solvent content 3.16 61.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 122.599 α = 90 b = 122.599 β = 90 c = 134.278 γ = 120
Symmetry Space Group P 32 2 1
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 MARRESEARCH 2007-07-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA SLS X10SA
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 2.8 45.27 100 0.1 16.7 5.6 29215 74.94
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) 1 2.8 2.95 100 0.85 3 5.6
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2ESM 2.8 41.24 27921 1262 100 0.198 0.196 0.244 0.2586 RANDOM 50.27
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] -0.02 -0.01 -0.02 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.862 r_dihedral_angle_4_deg 17.91 r_dihedral_angle_3_deg 15.328 r_scangle_it 6.441 r_dihedral_angle_1_deg 5.84 r_scbond_it 4.617 r_mcangle_it 2.751 r_mcbond_it 1.651 r_angle_refined_deg 1.294 r_angle_other_deg 0.862
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.862 r_dihedral_angle_4_deg 17.91 r_dihedral_angle_3_deg 15.328 r_scangle_it 6.441 r_dihedral_angle_1_deg 5.84 r_scbond_it 4.617 r_mcangle_it 2.751 r_mcbond_it 1.651 r_angle_refined_deg 1.294 r_angle_other_deg 0.862 r_symmetry_vdw_refined 0.227 r_nbd_refined 0.222 r_symmetry_vdw_other 0.215 r_nbtor_refined 0.189 r_nbd_other 0.184 r_xyhbond_nbd_refined 0.141 r_symmetry_hbond_refined 0.116 r_nbtor_other 0.088 r_chiral_restr 0.067 r_bond_refined_d 0.01 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5831 Nucleic Acid Atoms Solvent Atoms 9 Heterogen Atoms 60
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing