6YVP

Human histidine triad nucleotide-binding protein 2 (hHINT2) complexed with dGMP and refined to 2.77 A


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6YQD6YQD:B

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP28115 % (w/v) PEG6000, 5 % (v/v) glycerol

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 71.649α = 90
b = 36.531β = 103.034
c = 86.887γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 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
12.7742.3299.10.1980.2660.1760.9855.53.8569831.4
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)
12.772.9299.10.6680.8940.5890.79923.9

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 REPLACEMENTTHROUGHOUT6YQD:B2.7742.32569556598.6490.2180.20770.307734.978
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]
-1.8371.0865.134-3.431
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.661
r_dihedral_angle_3_deg19.373
r_dihedral_angle_4_deg18.269
r_dihedral_angle_1_deg6.486
r_lrange_it4.975
r_lrange_other4.973
r_mcangle_it2.68
r_mcangle_other2.679
r_scangle_other2.411
r_scangle_it2.409
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.661
r_dihedral_angle_3_deg19.373
r_dihedral_angle_4_deg18.269
r_dihedral_angle_1_deg6.486
r_lrange_it4.975
r_lrange_other4.973
r_mcangle_it2.68
r_mcangle_other2.679
r_scangle_other2.411
r_scangle_it2.409
r_mcbond_other1.577
r_mcbond_it1.576
r_angle_refined_deg1.491
r_scbond_it1.376
r_scbond_other1.373
r_angle_other_deg1.139
r_xyhbond_nbd_refined0.219
r_symmetry_nbd_other0.213
r_nbd_refined0.196
r_symmetry_xyhbond_nbd_refined0.19
r_nbd_other0.169
r_nbtor_refined0.153
r_symmetry_nbd_refined0.137
r_ncsr_local_group_10.126
r_symmetry_nbtor_other0.078
r_chiral_restr0.065
r_bond_refined_d0.005
r_gen_planes_refined0.004
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1756
Nucleic Acid Atoms
Solvent Atoms118
Heterogen Atoms46

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing