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Exploring backbone pattern in alpha/beta-peptide helix bundles: The GCN4-pLI side chain sequence on different (alpha-alpha-alpha-beta) backbones
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1GCM PDB ENTRY 1GCM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 298 0.1 M Tris pH 8.5, 25% v/v tert-butanol, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.01 38.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 31.817 α = 90 b = 43.082 β = 96 c = 37.001 γ = 90
Symmetry Space Group P 1 21 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 BRUKER SMART 6000 confocal mirrors 2007-04-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE BRUKER AXS MICROSTAR 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 2 22.84 97.8 0.047 20 4.4 6732
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.1 91.9 0.13 4.7 1.6
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 ENTRY 1GCM 2 22.84 6377 319 98 0.1592 0.15703 0.1569 0.20148 0.199 RANDOM 12.062
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] 0.42 -1.26 0.02 -0.71
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.724 r_dihedral_angle_4_deg 19.245 r_dihedral_angle_3_deg 13.774 r_dihedral_angle_1_deg 3.85 r_scangle_it 2.93 r_scbond_it 1.793 r_angle_refined_deg 1.644 r_angle_other_deg 1.163 r_mcangle_it 1.03 r_mcbond_it 0.649
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.724 r_dihedral_angle_4_deg 19.245 r_dihedral_angle_3_deg 13.774 r_dihedral_angle_1_deg 3.85 r_scangle_it 2.93 r_scbond_it 1.793 r_angle_refined_deg 1.644 r_angle_other_deg 1.163 r_mcangle_it 1.03 r_mcbond_it 0.649 r_symmetry_vdw_other 0.243 r_nbd_other 0.217 r_xyhbond_nbd_refined 0.186 r_symmetry_hbond_refined 0.186 r_nbd_refined 0.181 r_symmetry_vdw_refined 0.174 r_nbtor_refined 0.164 r_mcbond_other 0.153 r_chiral_restr 0.098 r_nbtor_other 0.079 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_bond_other_d 0.004 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 877 Nucleic Acid Atoms Solvent Atoms 130 Heterogen Atoms 38
Software Software Software Name Purpose PROTEUM PLUS data collection PHASER phasing REFMAC refinement PROTEUM PLUS data reduction PROTEUM PLUS data scaling