2VD5

Structure of Human Myotonic Dystrophy Protein Kinase in Complex with the Bisindoylmaleide inhibitor BIM VIII


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2ESMPDB ENTRY 2ESM

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
171M AMMONIUM SULPHATE, 1.5% PEG 3350, 0.1M BIS-TRIS PH7.0
Crystal Properties
Matthews coefficientSolvent content
3.1661.13

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 122.599α = 90
b = 122.599β = 90
c = 134.278γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2007-07-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SASLSX10SA

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
12.845.271000.116.75.62921574.94
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)
12.82.951000.8535.6

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 REPLACEMENTTHROUGHOUTPDB ENTRY 2ESM2.841.242792112621000.1980.1960.244RANDOM50.27
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]
-0.02-0.01-0.020.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.862
r_dihedral_angle_4_deg17.91
r_dihedral_angle_3_deg15.328
r_scangle_it6.441
r_dihedral_angle_1_deg5.84
r_scbond_it4.617
r_mcangle_it2.751
r_mcbond_it1.651
r_angle_refined_deg1.294
r_angle_other_deg0.862
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.862
r_dihedral_angle_4_deg17.91
r_dihedral_angle_3_deg15.328
r_scangle_it6.441
r_dihedral_angle_1_deg5.84
r_scbond_it4.617
r_mcangle_it2.751
r_mcbond_it1.651
r_angle_refined_deg1.294
r_angle_other_deg0.862
r_symmetry_vdw_refined0.227
r_nbd_refined0.222
r_symmetry_vdw_other0.215
r_nbtor_refined0.189
r_nbd_other0.184
r_xyhbond_nbd_refined0.141
r_symmetry_hbond_refined0.116
r_nbtor_other0.088
r_chiral_restr0.067
r_bond_refined_d0.01
r_gen_planes_refined0.004
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
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 AtomsNumber
Protein Atoms5831
Nucleic Acid Atoms
Solvent Atoms9
Heterogen Atoms60

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing