☰ Navigation Tabs
Exploring Cystine Dense Peptide Space to Open a Unique Molecular Toolbox
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1QK7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5 298 100 citrate pH = 5, 20% w/w PEG 6000
Crystal Properties Matthews coefficient Solvent content 1.92 35.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.639 α = 90 b = 50.639 β = 90 c = 20.104 γ = 120
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 2015-05-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.54
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) 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 1.89 50 97.5 0.058 0.059 58.11 25.9 2417
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.89 1.94 80.3 0.286 0.118 0.941 6.2
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 1QK7 1.89 43.85 2207 107 93.68 0.21801 0.21572 0.2241 0.26723 0.2874 RANDOM 29.265
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] -0.87 -0.43 -0.87 2.81
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_4_deg 24.086 r_dihedral_angle_2_deg 23.02 r_dihedral_angle_3_deg 17.476 r_dihedral_angle_1_deg 9.748 r_long_range_B_other 5.318 r_long_range_B_refined 5.317 r_scangle_other 4.302 r_mcangle_it 3.531 r_mcangle_other 3.524 r_scbond_it 2.931
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_4_deg 24.086 r_dihedral_angle_2_deg 23.02 r_dihedral_angle_3_deg 17.476 r_dihedral_angle_1_deg 9.748 r_long_range_B_other 5.318 r_long_range_B_refined 5.317 r_scangle_other 4.302 r_mcangle_it 3.531 r_mcangle_other 3.524 r_scbond_it 2.931 r_scbond_other 2.919 r_mcbond_it 2.431 r_mcbond_other 2.388 r_angle_refined_deg 1.717 r_angle_other_deg 0.925 r_chiral_restr 0.113 r_bond_refined_d 0.027 r_gen_planes_refined 0.012 r_bond_other_d 0.004 r_gen_planes_other 0.002 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 228 Nucleic Acid Atoms Solvent Atoms 18 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing