6YPR

Human histidine triad nucleotide-binding protein 2 (hHINT2) refined to 1.26 A in H32 space group


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52810.8 M Na/K Tartrate, 0.1 M HEPES 7.5
Crystal Properties
Matthews coefficientSolvent content
2.3647.84

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 72.076α = 90
b = 72.076β = 90
c = 103.576γ = 120
Symmetry
Space GroupH 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2016-10-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)1.0332PETRA III, EMBL c/o DESYP13 (MX1)

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
11.2636.04399.80.0580.0730.0430.99812.64.8281029.5
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)
11.261.2899.80.6450.8150.4920.68524.5

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 REPLACEMENTTHROUGHOUT3TW21.2636.04328101137599.730.1180.11710.142713.669
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]
-0.665-0.333-0.6652.159
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.908
r_dihedral_angle_4_deg17.379
r_dihedral_angle_3_deg11.131
r_rigid_bond_restr10.479
r_dihedral_angle_1_deg6.33
r_lrange_it4.609
r_scangle_it3.856
r_scangle_other3.854
r_lrange_other3.816
r_scbond_it3.354
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.908
r_dihedral_angle_4_deg17.379
r_dihedral_angle_3_deg11.131
r_rigid_bond_restr10.479
r_dihedral_angle_1_deg6.33
r_lrange_it4.609
r_scangle_it3.856
r_scangle_other3.854
r_lrange_other3.816
r_scbond_it3.354
r_scbond_other3.351
r_angle_refined_deg2.077
r_mcangle_it1.68
r_mcangle_other1.679
r_angle_other_deg1.611
r_mcbond_other1.345
r_mcbond_it1.342
r_symmetry_nbd_refined0.906
r_symmetry_xyhbond_nbd_refined0.403
r_nbd_refined0.211
r_symmetry_nbd_other0.208
r_nbtor_refined0.168
r_xyhbond_nbd_refined0.166
r_nbd_other0.162
r_chiral_restr0.141
r_symmetry_nbtor_other0.088
r_bond_refined_d0.018
r_symmetry_xyhbond_nbd_other0.015
r_gen_planes_refined0.014
r_bond_other_d0.01
r_gen_planes_other0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms756
Nucleic Acid Atoms
Solvent Atoms84
Heterogen Atoms18

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing