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Crystal structure of MLAV 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
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 2.44 49.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.817 α = 90 b = 62.817 β = 90 c = 65.799 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 IMAGE PLATE RIGAKU RAXIS IV Osmic Confocal Maxflux 2002-09-13 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 1.9 45.64 99.1 0.041 21.9 4.9 10799 10799 2.5 31.836
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 1.9 1.94 99.7 0.393
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 1BFS 1.901 45.64 10244 10244 519 99.09 0.184 0.184 0.182 0.195 0.222 0.2412 RANDOM 31.585
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] -0.07 -0.07 0.14
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 6.77 r_dihedral_angle_1_deg 6.693 r_mcangle_it 4.636 r_scbond_it 4.412 r_mcbond_it 3.118 r_angle_refined_deg 1.605 r_angle_other_deg 0.893 r_symmetry_hbond_refined 0.453 r_xyhbond_nbd_refined 0.368 r_nbd_other 0.264
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 6.77 r_dihedral_angle_1_deg 6.693 r_mcangle_it 4.636 r_scbond_it 4.412 r_mcbond_it 3.118 r_angle_refined_deg 1.605 r_angle_other_deg 0.893 r_symmetry_hbond_refined 0.453 r_xyhbond_nbd_refined 0.368 r_nbd_other 0.264 r_symmetry_vdw_other 0.252 r_symmetry_vdw_refined 0.192 r_nbd_refined 0.182 r_chiral_restr 0.107 r_nbtor_other 0.088 r_bond_refined_d 0.016 r_gen_planes_refined 0.007 r_gen_planes_other 0.003 r_bond_other_d 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 815 Nucleic Acid Atoms Solvent Atoms 124 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling AMoRE phasing REFMAC refinement