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Crystal structure of SU6656-bound calcium/calmodulin-dependent protein kinase II delta in complex with calmodulin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2VN9 PDB ENTRIES 2VN9, 1MXE experimental model PDB 1MXE PDB ENTRIES 2VN9, 1MXE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 0.1M SODIUM POTASSIUM PHOSPHATE, 20% PEG3350 10% ETHYLENE GLYCOL, pH 7.5
Crystal Properties Matthews coefficient Solvent content 2.6 52.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.26 α = 90 b = 68.85 β = 90 c = 121.98 γ = 90
Symmetry Space Group P 21 21 21
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 2008-07-24 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 1.9 33.13 99.7 0.11 10.8 4.9 45901 20.729
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 1.9 2 100 0.8 2.6 4.9
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 PDB ENTRIES 2VN9, 1MXE 1.9 33.34 45074 827 99.57 0.1613 0.16057 0.1803 0.19929 0.2142 RANDOM 16.066
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] -1.92 1.02 0.9
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.518 r_dihedral_angle_4_deg 18.403 r_dihedral_angle_3_deg 12.972 r_scangle_it 9.372 r_scbond_it 7.07 r_dihedral_angle_1_deg 5.207 r_mcangle_it 4.709 r_mcbond_it 3.306 r_angle_refined_deg 1.37 r_mcbond_other 1.101
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.518 r_dihedral_angle_4_deg 18.403 r_dihedral_angle_3_deg 12.972 r_scangle_it 9.372 r_scbond_it 7.07 r_dihedral_angle_1_deg 5.207 r_mcangle_it 4.709 r_mcbond_it 3.306 r_angle_refined_deg 1.37 r_mcbond_other 1.101 r_angle_other_deg 0.911 r_symmetry_hbond_refined 0.23 r_nbd_refined 0.216 r_nbtor_refined 0.177 r_nbd_other 0.17 r_symmetry_vdw_other 0.17 r_metal_ion_refined 0.163 r_symmetry_vdw_refined 0.163 r_xyhbond_nbd_refined 0.156 r_xyhbond_nbd_other 0.096 r_nbtor_other 0.087 r_chiral_restr 0.085 r_symmetry_hbond_other 0.047 r_bond_refined_d 0.015 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_metal_ion_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_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 3544 Nucleic Acid Atoms Solvent Atoms 405 Heterogen Atoms 64
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing