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GCN4 leucine zipper domain in a trimeric oligomerization state
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1IJ2 PDB entry 1IJ2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 298 0.2 M Ammonium Sulfate, 0.1 M MES buffer, 30% (w/v) PEG MME 5000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.2 44.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.179 α = 90 b = 34.379 β = 139.68 c = 78.117 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 RIGAKU SATURN 944 2011-09-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E SUPERBRIGHT 1.5418
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 2.2 50.54 99.5 0.094 9.7 2.71 5443
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 1IJ2 2.2 50.54 5198 244 99.34 0.22856 0.22582 0.28733 0.2366 RANDOM 24.676
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] -1.7 -1.78 0.93 -1.93
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.965 r_dihedral_angle_4_deg 18.803 r_dihedral_angle_3_deg 14.31 r_dihedral_angle_1_deg 4.211 r_angle_other_deg 4.042 r_angle_refined_deg 1.387 r_chiral_restr 0.072 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 r_gen_planes_other 0.004
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.965 r_dihedral_angle_4_deg 18.803 r_dihedral_angle_3_deg 14.31 r_dihedral_angle_1_deg 4.211 r_angle_other_deg 4.042 r_angle_refined_deg 1.387 r_chiral_restr 0.072 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 r_gen_planes_other 0.004 r_bond_other_d r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_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 828 Nucleic Acid Atoms Solvent Atoms 48 Heterogen Atoms 15
Software Software Software Name Purpose CrystalClear data collection PHASER phasing REFMAC refinement d*TREK data reduction d*TREK data scaling