1Z57

Crystal structure of human CLK1 in complex with 10Z-Hymenialdisine


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1JOW1JOW.pdb

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP9277PEG 6K, Bicine, pH 9.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
1.831.8

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 92.277α = 90
b = 64.434β = 119.19
c = 80.112γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2005-03-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SA0.9184SLSX10SA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.75099.845196
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.71.7586

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1JOW.pdb1.729.34077540775217395.010.140140.137650.18581RANDOM18.72
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]
0.480.46-0.580.55
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.84
r_dihedral_angle_4_deg20.028
r_dihedral_angle_3_deg11.532
r_sphericity_free7.032
r_scangle_it6.814
r_dihedral_angle_1_deg5.85
r_scbond_it5.216
r_mcangle_it4.35
r_sphericity_bonded3.696
r_mcbond_it3.679
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.84
r_dihedral_angle_4_deg20.028
r_dihedral_angle_3_deg11.532
r_sphericity_free7.032
r_scangle_it6.814
r_dihedral_angle_1_deg5.85
r_scbond_it5.216
r_mcangle_it4.35
r_sphericity_bonded3.696
r_mcbond_it3.679
r_rigid_bond_restr2.634
r_mcbond_other2.161
r_angle_refined_deg1.591
r_angle_other_deg0.845
r_symmetry_vdw_other0.325
r_nbd_refined0.221
r_nbd_other0.179
r_nbtor_refined0.176
r_symmetry_vdw_refined0.163
r_xyhbond_nbd_refined0.154
r_chiral_restr0.095
r_symmetry_hbond_refined0.095
r_nbtor_other0.084
r_bond_refined_d0.015
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
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
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2674
Nucleic Acid Atoms
Solvent Atoms401
Heterogen Atoms18

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing