6F23

Complex between MTH1 and compound 16 (a 4-amino-7-azaindole derivative)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3Q93 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP3.629323% PEG 6000, 0.28M lithium sulfate, 0.1M sodium acetate pH 3.6
Crystal Properties
Matthews coefficientSolvent content
2.2846.2

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 59.42α = 90
b = 67.08β = 90
c = 83.41γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-FToroidal mirror2014-11-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-10.972957ESRFID23-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)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
11.8448.499.70.1480.0630.9963.96.529541
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.841.999.31.8770.8320.5180.56

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 REPLACEMENTTHROUGHOUT3Q931.8448.428037144399.570.223050.221140.25872RANDOM30.885
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]
0.320.31-0.63
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.696
r_dihedral_angle_3_deg13.484
r_dihedral_angle_4_deg12.571
r_dihedral_angle_1_deg6.635
r_long_range_B_refined5.839
r_long_range_B_other5.839
r_angle_refined_deg1.559
r_scangle_other0.948
r_angle_other_deg0.889
r_scbond_it0.694
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.696
r_dihedral_angle_3_deg13.484
r_dihedral_angle_4_deg12.571
r_dihedral_angle_1_deg6.635
r_long_range_B_refined5.839
r_long_range_B_other5.839
r_angle_refined_deg1.559
r_scangle_other0.948
r_angle_other_deg0.889
r_scbond_it0.694
r_scbond_other0.694
r_mcangle_it0.432
r_mcangle_other0.432
r_mcbond_it0.253
r_mcbond_other0.253
r_chiral_restr0.087
r_bond_refined_d0.012
r_gen_planes_refined0.007
r_bond_other_d0.002
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2540
Nucleic Acid Atoms
Solvent Atoms199
Heterogen Atoms107

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing