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Crystal structure of MLAM 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 2.32 46.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.403 α = 90 b = 59.403 β = 90 c = 59.856 γ = 90
Symmetry Space Group P 41 21 2
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 ADSC QUANTUM 4 2002-02-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SRS BEAMLINE PX9.6 0.864 SRS PX9.6
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 2.699 42.26 99.8 0.042 17.5 7.4 3233 3233 2.5 75.4
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 2.699 2.76 100 0.347
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1BFS 2.699 42.26 2913 2913 295 99.6 0.265 0.265 0.259 0.2615 0.317 0.3302 RANDOM 56.978
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] 0.86 0.86 -1.71
RMS Deviations Key Refinement Restraint Deviation r_angle_other_deg 3.511 r_angle_refined_deg 1.59 r_dihedral_angle_1_deg 1.334 r_symmetry_vdw_other 0.381 r_nbd_other 0.3 r_nbd_refined 0.272 r_symmetry_vdw_refined 0.234 r_xyhbond_nbd_refined 0.22 r_symmetry_hbond_refined 0.177 r_nbtor_other 0.108
RMS Deviations Key Refinement Restraint Deviation r_angle_other_deg 3.511 r_angle_refined_deg 1.59 r_dihedral_angle_1_deg 1.334 r_symmetry_vdw_other 0.381 r_nbd_other 0.3 r_nbd_refined 0.272 r_symmetry_vdw_refined 0.234 r_xyhbond_nbd_refined 0.22 r_symmetry_hbond_refined 0.177 r_nbtor_other 0.108 r_chiral_restr 0.105 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_gen_planes_other 0.007 r_bond_other_d 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_it r_mcbond_other r_mcangle_it r_scbond_it r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 801 Nucleic Acid Atoms Solvent Atoms 13 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling AMoRE phasing REFMAC refinement