2H8R

Hepatocyte Nuclear Factor 1b bound to DNA: MODY5 Gene Product


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP82956%(v/v) PEG300, 5%(v/v) PEG8000, 8%(v/v) glycerol, 100mM Tris, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
3.3262.91

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 174.689α = 90
b = 174.689β = 90
c = 72.434γ = 120
Symmetry
Space GroupH 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2005-12-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-BM0.97923APS22-BM

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
13.227.993.90.0880.08328.86.3126351258257.24
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
3.23.3163.40.3130.2733.353.8

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1IC83.2202125821199263793.260.226140.222920.2899RANDOM69.209
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]
5.432.725.43-8.15
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free20.239
r_dihedral_angle_1_deg12.042
r_scangle_it8.674
r_scbond_it5.745
r_angle_refined_deg5.45
r_sphericity_bonded5.174
r_mcangle_it4.678
r_rigid_bond_restr3.686
r_mcbond_it2.542
r_symmetry_hbond_refined0.47
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free20.239
r_dihedral_angle_1_deg12.042
r_scangle_it8.674
r_scbond_it5.745
r_angle_refined_deg5.45
r_sphericity_bonded5.174
r_mcangle_it4.678
r_rigid_bond_restr3.686
r_mcbond_it2.542
r_symmetry_hbond_refined0.47
r_nbd_refined0.374
r_xyhbond_nbd_refined0.294
r_chiral_restr0.258
r_symmetry_vdw_refined0.236
r_bond_refined_d0.079
r_gen_planes_refined0.02
r_bond_other_d
r_angle_other_deg
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_gen_planes_other
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2916
Nucleic Acid Atoms814
Solvent Atoms7
Heterogen Atoms

Software

Software
Software NamePurpose
SERGUIdata collection
HKL-2000data reduction
MOLREPphasing
REFMACrefinement
HKL-2000data scaling