3QGZ

Re-investigated high resolution crystal structure of histidine triad nucleotide-binding protein 1 (HINT1) from rabbit complexed with adenosine


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1RZYPDB entry 1RZY

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.528125% PEG 8000, 0.1M cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 281K
Crystal Properties
Matthews coefficientSolvent content
2.0439.77

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 39.747α = 90
b = 39.747β = 90
c = 141.83γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mm2009-11-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONMAX II BEAMLINE I911-21.038MAX 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
11.139.7499.20.08718.717.547034-38.7
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)
11.11.1697.50.676413.56556

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-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONRIGID BODY REFINEMENTTHROUGHOUTPDB entry 1RZY1.138.2744545237198.970.143770.143770.14250.16772RANDOM17.569
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]
0.060.06-0.13
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.33
r_dihedral_angle_3_deg13.941
r_dihedral_angle_4_deg10.817
r_scangle_it7.054
r_dihedral_angle_1_deg6.24
r_scbond_it5.363
r_mcangle_it4.026
r_rigid_bond_restr2.894
r_mcbond_it2.755
r_angle_refined_deg2.489
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.33
r_dihedral_angle_3_deg13.941
r_dihedral_angle_4_deg10.817
r_scangle_it7.054
r_dihedral_angle_1_deg6.24
r_scbond_it5.363
r_mcangle_it4.026
r_rigid_bond_restr2.894
r_mcbond_it2.755
r_angle_refined_deg2.489
r_chiral_restr0.153
r_bond_refined_d0.027
r_gen_planes_refined0.015
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms873
Nucleic Acid Atoms
Solvent Atoms161
Heterogen Atoms19

Software

Software
Software NamePurpose
MAR345data collection
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
REFMACphasing