☰ Navigation Tabs
Structure of a triple-helix region of human Collagen type IV from Trautec
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1K6M
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 Index-E7 (0.05M MgCl2, 0.1M HEPES pH7.5, 30% PEG 550 MME)
Crystal Properties Matthews coefficient Solvent content 1.75 29.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 30.479 α = 90 b = 26.425 β = 99.088 c = 67.617 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 PIXEL DECTRIS EIGER X 9M 2024-03-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08ID-1 0.95300 CLSI 08ID-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) 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 1.3 33.38 98.8 0.993 9.7 6.4 26186
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.3 1.32 0.609
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.3 33.38 26160 1294 98.472 0.146 0.1437 0.1439 0.1971 0.1981 15.177
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] 0.373 -0.281 0.145 -0.408
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 19.399 r_lrange_it 15.081 r_lrange_other 13.375 r_scangle_it 9.687 r_scangle_other 9.681 r_dihedral_angle_3_deg 9.633 r_mcangle_other 7.985 r_mcangle_it 7.98 r_scbond_it 6.647 r_scbond_other 6.642
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 19.399 r_lrange_it 15.081 r_lrange_other 13.375 r_scangle_it 9.687 r_scangle_other 9.681 r_dihedral_angle_3_deg 9.633 r_mcangle_other 7.985 r_mcangle_it 7.98 r_scbond_it 6.647 r_scbond_other 6.642 r_dihedral_angle_2_deg 6.248 r_mcbond_it 5.538 r_mcbond_other 5.451 r_dihedral_angle_1_deg 5.374 r_rigid_bond_restr 4.135 r_angle_refined_deg 1.69 r_angle_other_deg 0.628 r_symmetry_xyhbond_nbd_refined 0.225 r_xyhbond_nbd_refined 0.219 r_chiral_restr_other 0.218 r_nbd_other 0.218 r_nbd_refined 0.206 r_nbtor_refined 0.184 r_symmetry_nbd_other 0.179 r_symmetry_nbd_refined 0.157 r_symmetry_nbtor_other 0.09 r_symmetry_xyhbond_nbd_other 0.07 r_chiral_restr 0.067 r_bond_refined_d 0.012 r_gen_planes_refined 0.008 r_bond_other_d 0.003 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1064 Nucleic Acid Atoms Solvent Atoms 235 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing