3IF7

Structure of Calmodulin complexed with its first endogenous inhibitor, sphingosylphosphorylcholine


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1LINN- and C-terminal domains of PDB entry 1LIN

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.529350mM 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 coefficientSolvent content
2.3146.84

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 39.669α = 90
b = 39.669β = 90
c = 170.34γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315rmirrors2008-07-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-10.9762ESRFID23-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.6301000.10512.38.62159621596-324.4
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.61.691000.4464.17.93047

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTN- and C-terminal domains of PDB entry 1LIN1.629.392042620426110399.980.194590.194590.192320.23825RANDOM34.758
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]
0.420.210.42-0.63
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.967
r_dihedral_angle_4_deg21.654
r_dihedral_angle_3_deg14.874
r_scangle_it6.469
r_dihedral_angle_1_deg5.323
r_scbond_it3.897
r_mcangle_it2.965
r_angle_refined_deg2.085
r_mcbond_it1.765
r_angle_other_deg1.113
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.967
r_dihedral_angle_4_deg21.654
r_dihedral_angle_3_deg14.874
r_scangle_it6.469
r_dihedral_angle_1_deg5.323
r_scbond_it3.897
r_mcangle_it2.965
r_angle_refined_deg2.085
r_mcbond_it1.765
r_angle_other_deg1.113
r_mcbond_other0.578
r_chiral_restr0.134
r_bond_refined_d0.025
r_gen_planes_refined0.009
r_bond_other_d0.005
r_gen_planes_other0.001
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 AtomsNumber
Protein Atoms1083
Nucleic Acid Atoms
Solvent Atoms79
Heterogen Atoms84

Software

Software
Software NamePurpose
ADSCdata collection
MOLREPphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling