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Protein kinase MK2 in complex with an inhibitor (crystal form-1, soaking)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1NY3 PDB ENTRY 1NY3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 4.5 1.5-1.6M SODIUM POTASSIUM PHOSPHATE PH 4.5, 0.014M DEOXY-BIGCHAP. THE INHIBITOR WAS SOAKED INTO CRYSTALS GROWN INITIALLY FROM MK2-ADP
Crystal Properties Matthews coefficient Solvent content 4.5 72.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 253.959 α = 90 b = 253.959 β = 90 c = 253.959 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 MARRESEARCH 2005-01-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA SLS X06SA
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 3.1 48.9 99.8 0.08 27.1 7.8 13232 87.6
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 3.1 3.15 100 0.66 4 8.2
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 FOURIER SYNTHESIS THROUGHOUT PDB ENTRY 1NY3 3.1 48.9 12482 722 99.7 0.232 0.23 0.274 0.2448 RANDOM 72.47
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 40.472 r_dihedral_angle_4_deg 29.582 r_dihedral_angle_3_deg 22.55 r_dihedral_angle_1_deg 7.265 r_scangle_it 3.51 r_scbond_it 2.013 r_angle_refined_deg 1.706 r_mcangle_it 1.504 r_mcbond_it 0.863 r_nbtor_refined 0.336
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.472 r_dihedral_angle_4_deg 29.582 r_dihedral_angle_3_deg 22.55 r_dihedral_angle_1_deg 7.265 r_scangle_it 3.51 r_scbond_it 2.013 r_angle_refined_deg 1.706 r_mcangle_it 1.504 r_mcbond_it 0.863 r_nbtor_refined 0.336 r_symmetry_vdw_refined 0.258 r_nbd_refined 0.253 r_symmetry_hbond_refined 0.185 r_xyhbond_nbd_refined 0.147 r_chiral_restr 0.114 r_bond_refined_d 0.017 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_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 2385 Nucleic Acid Atoms Solvent Atoms 9 Heterogen Atoms 31
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling CNX phasing