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Crystal Structure of the Cofactor-Binding Domain of the Cbl Transcriptional Regulator
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1AL3 PDB ENTRY 1AL3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 292 3.8 M NaCl, 10 mM Adenosine 5'-Phosphosulphate, 0.1M Hepes, pH 7.50, temperature 292K
Crystal Properties Matthews coefficient Solvent content 5.09 75.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 169.686 α = 90 b = 242.373 β = 90 c = 101.626 γ = 90
Symmetry Space Group C 2 2 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 CCD MARRESEARCH TRIANGULAR MONOCHROMATOR, BENT MIRROR 2004-02-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X13 EMBL/DESY, HAMBURG X13
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 2.8 30 99.6 0.124 0.092 10.4 3.9 51701 -1.5 39.6
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) 1 2.8 2.9 97.6 0.566 0.639 2.4 3.8
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 (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 1AL3 2.8 30 49173 46596 2577 99.7 0.187 0.184 0.1864 0.226 0.1833 RANDOM 39.6
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] -1.98 2.4 -0.42
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.309 r_dihedral_angle_3_deg 19.774 r_dihedral_angle_4_deg 19.567 r_dihedral_angle_1_deg 9.055 r_mcangle_it 2.232 r_scangle_it 2.133 r_angle_refined_deg 1.803 r_scbond_it 1.266 r_mcbond_it 1.261 r_nbtor_refined 0.337
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.309 r_dihedral_angle_3_deg 19.774 r_dihedral_angle_4_deg 19.567 r_dihedral_angle_1_deg 9.055 r_mcangle_it 2.232 r_scangle_it 2.133 r_angle_refined_deg 1.803 r_scbond_it 1.266 r_mcbond_it 1.261 r_nbtor_refined 0.337 r_symmetry_hbond_refined 0.301 r_symmetry_vdw_refined 0.264 r_nbd_refined 0.253 r_xyhbond_nbd_refined 0.214 r_chiral_restr 0.112 r_bond_refined_d 0.016 r_gen_planes_refined 0.006 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7125 Nucleic Acid Atoms Solvent Atoms 380 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing