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Structure of Calmodulin complexed with its first endogenous inhibitor, sphingosylphosphorylcholine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1LIN N- and C-terminal domains of PDB entry 1LIN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 293 50mM sodium cacodylate, 10mM CaCl2, 10mM MgCl2, 28% PEG 8000: Mixed with 10mM lipid in methanol solution and 1mM protein solution, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.31 46.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.669 α = 90 b = 39.669 β = 90 c = 170.34 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 ADSC QUANTUM 315r mirrors 2008-07-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.9762 ESRF ID23-1
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 1.6 30 100 0.105 12.3 8.6 21596 21596 -3 24.4
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 1.6 1.69 100 0.446 4.1 7.9 3047
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 N- and C-terminal domains of PDB entry 1LIN 1.6 29.39 20426 20426 1103 99.98 0.19459 0.19459 0.19232 0.2018 0.23825 0.2433 RANDOM 34.758
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] 0.42 0.21 0.42 -0.63
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.967 r_dihedral_angle_4_deg 21.654 r_dihedral_angle_3_deg 14.874 r_scangle_it 6.469 r_dihedral_angle_1_deg 5.323 r_scbond_it 3.897 r_mcangle_it 2.965 r_angle_refined_deg 2.085 r_mcbond_it 1.765 r_angle_other_deg 1.113
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.967 r_dihedral_angle_4_deg 21.654 r_dihedral_angle_3_deg 14.874 r_scangle_it 6.469 r_dihedral_angle_1_deg 5.323 r_scbond_it 3.897 r_mcangle_it 2.965 r_angle_refined_deg 2.085 r_mcbond_it 1.765 r_angle_other_deg 1.113 r_mcbond_other 0.578 r_chiral_restr 0.134 r_bond_refined_d 0.025 r_gen_planes_refined 0.009 r_bond_other_d 0.005 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1083 Nucleic Acid Atoms Solvent Atoms 79 Heterogen Atoms 84
Software Software Software Name Purpose ADSC data collection MOLREP phasing REFMAC refinement MOSFLM data reduction SCALA data scaling