3MDB

Crystal structure of the ternary complex of full length centaurin alpha-1, KIF13B FHA domain, and IP4


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3FM8nearly isomorphous coordinates of PDB entry 3FM8

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6291Sample buffer: 20mM HEPES, pH 7.30, 500mM NaCl, 1mM TCEP, 5% Glycerol. Protein complex was mixed with PIP3 in 1:1 molar ratio and acetone (5%). Reservoir solution: 0.8M lithium sulfate, 0.5M ammonium sulfate, 0.1M sodium citrate. Cryo-protectant: 2.0M lithium sulfate., vapor diffusion, sitting drop, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.6658.2

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 115.797α = 90
b = 115.797β = 90
c = 189.269γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR3002008-10-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-B0.97625APS23-ID-B

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
12.95301000.1396.414.627800
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)
12.953.061000.95714.72716

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTnearly isomorphous coordinates of PDB entry 3FM82.95229.4372773697899.9640.2270.2250.277thin shells51.231
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]
0.6090.609-1.218
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.67
r_dihedral_angle_4_deg17.559
r_dihedral_angle_3_deg15.777
r_dihedral_angle_1_deg5.974
r_mcangle_it1.994
r_scangle_it1.421
r_angle_refined_deg1.158
r_mcbond_it1.136
r_scbond_it0.86
r_angle_other_deg0.806
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.67
r_dihedral_angle_4_deg17.559
r_dihedral_angle_3_deg15.777
r_dihedral_angle_1_deg5.974
r_mcangle_it1.994
r_scangle_it1.421
r_angle_refined_deg1.158
r_mcbond_it1.136
r_scbond_it0.86
r_angle_other_deg0.806
r_mcbond_other0.143
r_chiral_restr0.068
r_bond_refined_d0.011
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7066
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms41

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data scaling