☰ Navigation Tabs
Crystal structure of YLGV mutant of dimerisation domain of NF-kB p50 transcription factor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1BFS PDB ENTRY 1BFS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 292 PEG 8000, ammonium sulphate, cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Crystal Properties Matthews coefficient Solvent content 1.96 36.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.602 α = 90 b = 73.586 β = 90 c = 138.864 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE RIGAKU RAXIS IV OSMIC MIRRORS 2002-01-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RUH3R 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.2 69.01 98.3 0.065 14.6 5.1 20980 20980 2.5 29.295
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 2.2 2.25 96 0.281
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1BFS 2.202 69.01 19850 19850 1081 98.28 0.176 0.176 0.173 0.235 0.2219 RANDOM 23.24
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] -0.88 -0.32 1.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.622 r_scangle_it 5.172 r_mcangle_it 4.004 r_scbond_it 3.682 r_mcbond_it 3.015 r_angle_refined_deg 1.522 r_angle_other_deg 0.864 r_symmetry_vdw_other 0.333 r_nbd_other 0.255 r_symmetry_hbond_refined 0.238
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.622 r_scangle_it 5.172 r_mcangle_it 4.004 r_scbond_it 3.682 r_mcbond_it 3.015 r_angle_refined_deg 1.522 r_angle_other_deg 0.864 r_symmetry_vdw_other 0.333 r_nbd_other 0.255 r_symmetry_hbond_refined 0.238 r_xyhbond_nbd_refined 0.22 r_symmetry_vdw_refined 0.211 r_nbd_refined 0.193 r_chiral_restr 0.098 r_nbtor_other 0.085 r_bond_refined_d 0.018 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.002 r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_nbtor_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3306 Nucleic Acid Atoms Solvent Atoms 385 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling AMoRE phasing REFMAC refinement