☰ Navigation Tabs
Crystal Structure of the Nanog Homeodomain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1IG7 PDB ENTRY 1IG7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7 PEG3350, pH 7
Crystal Properties Matthews coefficient Solvent content 3.09 60.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 105.318 α = 90 b = 114.771 β = 98.68 c = 62.771 γ = 90
Symmetry Space Group C 1 2 1
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 MARRESEARCH 2007-04-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B APS 23-ID-B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.6 50 91 0.07 17.4 3.7 20786 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.6 2.64 68.9 0.52 2.4 2.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 1IG7 2.6 50 19601 1040 90.8 0.223 0.221 0.2109 0.265 0.2514 RANDOM 52.73
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] -2.24 -2.23 -2.7 4.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.908 r_dihedral_angle_3_deg 19.611 r_dihedral_angle_4_deg 13.873 r_dihedral_angle_1_deg 4.777 r_scangle_it 1.971 r_scbond_it 1.231 r_angle_refined_deg 1.193 r_mcangle_it 0.878 r_mcbond_it 0.485 r_symmetry_vdw_refined 0.399
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.908 r_dihedral_angle_3_deg 19.611 r_dihedral_angle_4_deg 13.873 r_dihedral_angle_1_deg 4.777 r_scangle_it 1.971 r_scbond_it 1.231 r_angle_refined_deg 1.193 r_mcangle_it 0.878 r_mcbond_it 0.485 r_symmetry_vdw_refined 0.399 r_nbtor_refined 0.298 r_nbd_refined 0.207 r_symmetry_hbond_refined 0.188 r_xyhbond_nbd_refined 0.14 r_chiral_restr 0.079 r_bond_refined_d 0.011 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other 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 r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3763 Nucleic Acid Atoms Solvent Atoms 69 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling PHASER phasing