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Crystal structure of human calmodulin-dependent protein kinase 1D
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1A06 PDB ENTRY 1A06
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 0.1M CITRATE PH 5.6, 20% ISOPROPANOL, 20% PEG 4K.
Crystal Properties Matthews coefficient Solvent content 2.59 52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.64 α = 90 b = 93.06 β = 96.16 c = 101.86 γ = 90
Symmetry Space Group P 1 21 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 MIRROR 2006-11-27 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 2.3 42.2 91.6 0.1 11.17 3.47 29986 2
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 2.3 2.4 99.9 0.44 2.56 3.8
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 ENTRY 1A06 2.3 101.02 28455 1514 91.6 0.189 0.186 0.1887 0.248 0.245 RANDOM 11.63
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] -0.79 -0.23 0.12 0.63
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.54 r_dihedral_angle_4_deg 23.345 r_dihedral_angle_3_deg 17.519 r_dihedral_angle_1_deg 9.291 r_scangle_it 8.199 r_scbond_it 6.697 r_mcangle_it 4.339 r_mcbond_it 3.182 r_angle_refined_deg 1.428 r_angle_other_deg 0.917
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.54 r_dihedral_angle_4_deg 23.345 r_dihedral_angle_3_deg 17.519 r_dihedral_angle_1_deg 9.291 r_scangle_it 8.199 r_scbond_it 6.697 r_mcangle_it 4.339 r_mcbond_it 3.182 r_angle_refined_deg 1.428 r_angle_other_deg 0.917 r_symmetry_vdw_other 0.218 r_symmetry_hbond_refined 0.199 r_nbd_other 0.19 r_nbd_refined 0.189 r_nbtor_refined 0.18 r_xyhbond_nbd_refined 0.173 r_symmetry_vdw_refined 0.106 r_nbtor_other 0.089 r_chiral_restr 0.085 r_bond_refined_d 0.013 r_gen_planes_refined 0.005 r_bond_other_d 0.004 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 4367 Nucleic Acid Atoms Solvent Atoms 188 Heterogen Atoms 46
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing