3O1X

High resolution crystal structure of histidine triad nucleotide-binding protein 1 (Hint1) C84A mutant from rabbit complexed with adenosine


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3LLJPDB ENTRY 3LLJ

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.528130% PEG 8000, 0.1M sodium cacodylate pH 6.5, O.1M sodium acetate, protein concentration 10 mg/ml, VAPOR DIFFUSION, HANGING DROP, temperature 281K
Crystal Properties
Matthews coefficientSolvent content
2.0439.79

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 39.765α = 90
b = 39.765β = 90
c = 141.41γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mmmirrors2009-11-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONMAX II BEAMLINE I911-21.0379MAX III911-2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
11.085099.60.1116.1510.749845-311
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.081.199.70.6282.887.32434

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 3LLJ1.0823.054992447232252299.680.142960.142960.141460.17139RANDOM23.216
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]
0.110.11-0.21
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.686
r_dihedral_angle_3_deg13.562
r_dihedral_angle_4_deg10.595
r_scangle_it6.684
r_dihedral_angle_1_deg6.219
r_scbond_it4.802
r_mcangle_it3.808
r_mcbond_it2.664
r_rigid_bond_restr2.583
r_angle_refined_deg2.272
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.686
r_dihedral_angle_3_deg13.562
r_dihedral_angle_4_deg10.595
r_scangle_it6.684
r_dihedral_angle_1_deg6.219
r_scbond_it4.802
r_mcangle_it3.808
r_mcbond_it2.664
r_rigid_bond_restr2.583
r_angle_refined_deg2.272
r_chiral_restr0.136
r_bond_refined_d0.025
r_gen_planes_refined0.013
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms883
Nucleic Acid Atoms
Solvent Atoms210
Heterogen Atoms20

Software

Software
Software NamePurpose
MAR345data collection
MOLREPphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling