3O1C

High resolution crystal structure of histidine triad nucleotide-binding protein 1 (Hint1) C38A 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 DROP6.528120% PEG 8000, 0.1M sodium acetate, 0.1M sodium cacodylate pH 6.5, protein concentration 10 mg/ml, VAPOR DIFFUSION, HANGING DROP, temperature 281K
Crystal Properties
Matthews coefficientSolvent content
2.0740.51

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 39.965α = 90
b = 39.965β = 90
c = 141.7γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX-225mirrors2009-09-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.10.91841BESSY14.1

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
11.0828.2696.70.06626.319.948586-39.5
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)
1.081.1494.20.556514.395611

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 3LLJ1.0828.265049446067248196.150.133350.133350.131820.16285RANDOM20.525
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]
0.080.08-0.15
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.477
r_dihedral_angle_3_deg13.316
r_dihedral_angle_4_deg12.47
r_scangle_it7.385
r_dihedral_angle_1_deg6.541
r_scbond_it5.621
r_mcangle_it4.874
r_mcbond_it3.314
r_angle_refined_deg2.371
r_rigid_bond_restr1.972
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.477
r_dihedral_angle_3_deg13.316
r_dihedral_angle_4_deg12.47
r_scangle_it7.385
r_dihedral_angle_1_deg6.541
r_scbond_it5.621
r_mcangle_it4.874
r_mcbond_it3.314
r_angle_refined_deg2.371
r_rigid_bond_restr1.972
r_chiral_restr0.147
r_bond_refined_d0.028
r_gen_planes_refined0.015
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms883
Nucleic Acid Atoms
Solvent Atoms204
Heterogen Atoms21

Software

Software
Software NamePurpose
MAR345data collection
MOLREPphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling