6YQM

Human histidine triad nucleotide-binding protein 1 (hHINT1) complexed with dGMP and refined to 1.02 A


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3TW2 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.728116 % (w/v) PEG 4000, 0.1 M sodium cacodylate
Crystal Properties
Matthews coefficientSolvent content
2.3146.83

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 78.658α = 90
b = 46.434β = 94.244
c = 64.102γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 2M2020-03-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.20.9184BESSY14.2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)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
11.0239.96399.10.0420.0560.0370.99914.13.81160205.1
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.021.0493.60.4660.630.4220.7852.13.3

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT3TW21.0239.96116016612899.0560.1130.11180.135611.705
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]
-0.117-0.011-0.0470.163
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.209
r_dihedral_angle_4_deg14.186
r_dihedral_angle_3_deg12.428
r_rigid_bond_restr8.289
r_lrange_it7.017
r_lrange_other7.016
r_dihedral_angle_1_deg6.398
r_mcbond_other5.931
r_mcbond_it5.926
r_mcangle_it5.524
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.209
r_dihedral_angle_4_deg14.186
r_dihedral_angle_3_deg12.428
r_rigid_bond_restr8.289
r_lrange_it7.017
r_lrange_other7.016
r_dihedral_angle_1_deg6.398
r_mcbond_other5.931
r_mcbond_it5.926
r_mcangle_it5.524
r_mcangle_other5.524
r_scangle_it4.804
r_scangle_other4.802
r_scbond_it4.508
r_scbond_other4.506
r_angle_refined_deg2.403
r_angle_other_deg1.991
r_nbd_other0.369
r_nbd_refined0.323
r_xyhbond_nbd_refined0.273
r_symmetry_nbd_refined0.27
r_symmetry_xyhbond_nbd_refined0.213
r_symmetry_nbd_other0.202
r_nbtor_refined0.173
r_chiral_restr0.143
r_symmetry_nbtor_other0.102
r_bond_refined_d0.026
r_bond_other_d0.021
r_gen_planes_refined0.012
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1773
Nucleic Acid Atoms
Solvent Atoms483
Heterogen Atoms30

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing