6YQD

Human histidine triad nucleotide-binding protein 2 (hHINT2) refined to 1.41 A in P212121 space group


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.52818 % w/v PEG8000, 0.1 M Tris-HCl
Crystal Properties
Matthews coefficientSolvent content
2.2845.96

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 37.921α = 90
b = 74.113β = 90
c = 77.249γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2018-12-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)0.9763PETRA 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
11.40777.2598.80.0730.0790.030.99918.212.54252211.6
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)
11.4071.4375.70.7150.8460.4390.7552.1

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 REPLACEMENTTHROUGHOUT3TW21.40753.4842457209298.6730.1020.10030.142817.947
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]
-0.7710.1820.589
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.084
r_dihedral_angle_4_deg16.681
r_dihedral_angle_3_deg12.144
r_dihedral_angle_1_deg6.291
r_scangle_it5.603
r_scangle_other5.602
r_rigid_bond_restr5.325
r_lrange_it5.219
r_scbond_it5.21
r_scbond_other5.21
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.084
r_dihedral_angle_4_deg16.681
r_dihedral_angle_3_deg12.144
r_dihedral_angle_1_deg6.291
r_scangle_it5.603
r_scangle_other5.602
r_rigid_bond_restr5.325
r_lrange_it5.219
r_scbond_it5.21
r_scbond_other5.21
r_lrange_other4.384
r_mcangle_it2.463
r_mcangle_other2.463
r_angle_refined_deg2.008
r_mcbond_other1.989
r_mcbond_it1.988
r_angle_other_deg1.665
r_nbd_refined0.266
r_symmetry_nbd_other0.201
r_symmetry_nbd_refined0.191
r_nbd_other0.189
r_xyhbond_nbd_refined0.171
r_nbtor_refined0.164
r_chiral_restr0.142
r_symmetry_xyhbond_nbd_refined0.109
r_symmetry_nbtor_other0.087
r_bond_refined_d0.017
r_gen_planes_refined0.012
r_bond_other_d0.005
r_gen_planes_other0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1685
Nucleic Acid Atoms
Solvent Atoms257
Heterogen Atoms1

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing