6YI0

Human histidine triad nucleotide-binding protein 2 (hHINT2) refined to 1.65 A in P41212 space group


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP29820% (v/v) ethylene glycol, 5% (w/v) PEG 3350, 20 mM MgCl2
Crystal Properties
Matthews coefficientSolvent content
2.2244.62

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 76.945α = 90
b = 76.945β = 90
c = 140.454γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX-2252014-12-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.20.91841BESSY14.2

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
11.6546.821000.0770.0840.0350.99915.310.85157619.5
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)
11.651.681001.0821.1910.4960.822.111

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 REPLACEMENTTHROUGHOUT3TW21.6543.04451490260899.9570.1870.18450.233133.062
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]
-1.569-1.5693.138
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.036
r_dihedral_angle_3_deg14.41
r_dihedral_angle_4_deg13.157
r_dihedral_angle_1_deg7.189
r_lrange_it6.112
r_lrange_other6.022
r_scangle_it4.387
r_scangle_other4.387
r_mcangle_it3.703
r_mcangle_other3.703
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.036
r_dihedral_angle_3_deg14.41
r_dihedral_angle_4_deg13.157
r_dihedral_angle_1_deg7.189
r_lrange_it6.112
r_lrange_other6.022
r_scangle_it4.387
r_scangle_other4.387
r_mcangle_it3.703
r_mcangle_other3.703
r_scbond_it2.947
r_scbond_other2.947
r_mcbond_other2.758
r_mcbond_it2.757
r_angle_refined_deg1.586
r_angle_other_deg1.33
r_metal_ion_refined0.353
r_symmetry_nbd_refined0.257
r_symmetry_metal_ion_refined0.242
r_nbd_other0.226
r_xyhbond_nbd_refined0.205
r_nbd_refined0.2
r_symmetry_nbd_other0.184
r_symmetry_xyhbond_nbd_refined0.176
r_nbtor_refined0.154
r_chiral_restr0.084
r_symmetry_nbtor_other0.082
r_symmetry_xyhbond_nbd_other0.067
r_bond_refined_d0.009
r_gen_planes_refined0.008
r_gen_planes_other0.003
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3308
Nucleic Acid Atoms
Solvent Atoms381
Heterogen Atoms1

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing