6YPX

Human histidine triad nucleotide-binding protein 2 (hHINT2) refined to 2.11 A in C2221 space group


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.52810.2 M sodium citrate, 0.1 M sodium cacodylate, 30 % 2-propanol
Crystal Properties
Matthews coefficientSolvent content
3.9969.15

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 138.411α = 90
b = 153.992β = 90
c = 74.785γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2013-07-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)0.9669PETRA 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
12.11102.9499.60.220.240.0940.99411.312.24616415.482
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)
12.112.1796.41.0411.1940.5680.69727.4

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 REPLACEMENTTHROUGHOUT3TW22.11102.9446144234999.590.1490.14760.184525.345
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]
0.1051.922-2.027
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.528
r_dihedral_angle_4_deg19.916
r_dihedral_angle_3_deg13.285
r_lrange_it7.575
r_lrange_other7.256
r_dihedral_angle_1_deg6.592
r_scangle_it4.936
r_scangle_other4.935
r_scbond_it3.242
r_scbond_other3.242
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.528
r_dihedral_angle_4_deg19.916
r_dihedral_angle_3_deg13.285
r_lrange_it7.575
r_lrange_other7.256
r_dihedral_angle_1_deg6.592
r_scangle_it4.936
r_scangle_other4.935
r_scbond_it3.242
r_scbond_other3.242
r_mcangle_it2.988
r_mcangle_other2.988
r_mcbond_it2.021
r_mcbond_other2.018
r_angle_refined_deg1.613
r_angle_other_deg1.407
r_nbd_refined0.229
r_nbd_other0.207
r_symmetry_xyhbond_nbd_refined0.201
r_xyhbond_nbd_refined0.185
r_symmetry_nbd_other0.184
r_nbtor_refined0.158
r_symmetry_nbd_refined0.136
r_ncsr_local_group_10.092
r_chiral_restr0.088
r_ncsr_local_group_60.086
r_ncsr_local_group_30.085
r_ncsr_local_group_50.083
r_symmetry_nbtor_other0.081
r_ncsr_local_group_20.081
r_ncsr_local_group_40.071
r_bond_refined_d0.012
r_gen_planes_refined0.008
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3532
Nucleic Acid Atoms
Solvent Atoms674
Heterogen Atoms24

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing