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Oxime side-chain cross-links in the GCN4-p1 dimeric coiled coil: Linear precursor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2ZTA PDB 2ZTA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 298 0.1 M sodium acetate pH 4.6, 1.6 M sodium chloride, 5% w/v PEG 1500, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.41 49.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.729 α = 90 b = 30.907 β = 97.75 c = 33.306 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 Rigaku VariMax Optics 2012-04-12 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 2.3 50 99.7 0.106 20.2 4.7 3576
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB 2ZTA 2.3 25 3307 232 99.41 0.2064 0.20201 0.2021 0.26809 0.2687 RANDOM 30.245
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] -0.52 1.76 -0.5 1.49
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.535 r_dihedral_angle_4_deg 20.903 r_dihedral_angle_3_deg 19.857 r_dihedral_angle_1_deg 4.287 r_angle_refined_deg 1.264 r_angle_other_deg 0.907 r_chiral_restr 0.065 r_bond_refined_d 0.012 r_bond_other_d 0.005 r_gen_planes_refined 0.004
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.535 r_dihedral_angle_4_deg 20.903 r_dihedral_angle_3_deg 19.857 r_dihedral_angle_1_deg 4.287 r_angle_refined_deg 1.264 r_angle_other_deg 0.907 r_chiral_restr 0.065 r_bond_refined_d 0.012 r_bond_other_d 0.005 r_gen_planes_refined 0.004 r_gen_planes_other 0.001 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 510 Nucleic Acid Atoms Solvent Atoms 36 Heterogen Atoms 18
Software Software Software Name Purpose CrystalClear data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling