6G9Z

Crystal structure of human histidine triad nucleotide-binding protein 1 (hHINT1) crystallized at P212121 space group, with visible extended fragment of N-terminus


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP728125% PEG 1500, 0.1 M MMT Buffer pH 7.0
Crystal Properties
Matthews coefficientSolvent content
2.5551.72

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 46.075α = 90
b = 63.379β = 90
c = 76.836γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2016-04-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.10.918409BESSY14.1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim 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
11.4339.5296.10.1370.1610.9948.783.774095415
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.431.5192.70.7030.8210.8331.963.74

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 REPLACEMENTTHROUGHOUT3TW21.4339.5238759204195.820.22630.223620.27726RANDOM9.995
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]
-0.730.290.44
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.442
r_sphericity_free30.801
r_dihedral_angle_4_deg15.412
r_dihedral_angle_3_deg14.09
r_sphericity_bonded12.113
r_dihedral_angle_1_deg6.676
r_long_range_B_refined4.388
r_long_range_B_other3.698
r_rigid_bond_restr3.457
r_scangle_other2.559
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.442
r_sphericity_free30.801
r_dihedral_angle_4_deg15.412
r_dihedral_angle_3_deg14.09
r_sphericity_bonded12.113
r_dihedral_angle_1_deg6.676
r_long_range_B_refined4.388
r_long_range_B_other3.698
r_rigid_bond_restr3.457
r_scangle_other2.559
r_mcangle_it2.323
r_mcangle_other2.323
r_mcbond_it2.118
r_mcbond_other2.117
r_scbond_other1.928
r_scbond_it1.927
r_angle_refined_deg1.812
r_angle_other_deg0.61
r_chiral_restr0.096
r_bond_refined_d0.016
r_gen_planes_refined0.01
r_gen_planes_other0.002
r_bond_other_d0.001
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
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1841
Nucleic Acid Atoms
Solvent Atoms401
Heterogen Atoms9

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
MOLREPphasing