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Hepatocyte Nuclear Factor 1b bound to DNA: MODY5 Gene Product
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1IC8 PDB ENTRY 1IC8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 295 6%(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 coefficient Solvent content 3.32 62.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 174.689 α = 90 b = 174.689 β = 90 c = 72.434 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MARMOSAIC 225 mm CCD 2005-12-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-BM 0.97923 APS 22-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) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 3.2 27.9 93.9 0.088 0.083 28.8 6.3 12635 12582 57.24
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) Redundancy Number Unique Reflections (All) 3.2 3.31 63.4 0.313 0.273 3.35 3.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1IC8 3.2 20 2 12582 11992 637 93.26 0.22614 0.22292 0.1945 0.2899 0.2639 RANDOM 69.209
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] 5.43 2.72 5.43 -8.15
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 20.239 r_dihedral_angle_1_deg 12.042 r_scangle_it 8.674 r_scbond_it 5.745 r_angle_refined_deg 5.45 r_sphericity_bonded 5.174 r_mcangle_it 4.678 r_rigid_bond_restr 3.686 r_mcbond_it 2.542 r_symmetry_hbond_refined 0.47
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 20.239 r_dihedral_angle_1_deg 12.042 r_scangle_it 8.674 r_scbond_it 5.745 r_angle_refined_deg 5.45 r_sphericity_bonded 5.174 r_mcangle_it 4.678 r_rigid_bond_restr 3.686 r_mcbond_it 2.542 r_symmetry_hbond_refined 0.47 r_nbd_refined 0.374 r_xyhbond_nbd_refined 0.294 r_chiral_restr 0.258 r_symmetry_vdw_refined 0.236 r_bond_refined_d 0.079 r_gen_planes_refined 0.02 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 Atoms Number Protein Atoms 2916 Nucleic Acid Atoms 814 Solvent Atoms 7 Heterogen Atoms
Software Software Software Name Purpose SERGUI data collection HKL-2000 data reduction MOLREP phasing REFMAC refinement HKL-2000 data scaling