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Structure of a triple-helix region of human collagen type III from Trautec
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2CUO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.2M MgAc2, 0.1M Na cacodylate pH6.5, 20% PEG 8000
Crystal Properties Matthews coefficient Solvent content 1.79 31.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 18.582 α = 90 b = 19.32 β = 96.886 c = 74.234 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 PILATUS3 6M 2022-01-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08ID-1 0.7749 CLSI 08ID-1
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 1.3 36.85 99.9 0.02 58.8 6.5 13244
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.3 1.32 0.041
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2cuo 1.3 24.578 13236 629 99.887 0.116 0.1144 0.1143 0.1582 0.1578 13.945
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] -0.08 -0.299 -0.012 0.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 18.853 r_dihedral_angle_3_deg 10.525 r_dihedral_angle_4_deg 10.07 r_rigid_bond_restr 8.076 r_dihedral_angle_1_deg 5.872 r_lrange_it 4.249 r_lrange_other 4.051 r_scangle_it 3.559 r_scangle_other 3.55 r_scbond_it 2.963
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 18.853 r_dihedral_angle_3_deg 10.525 r_dihedral_angle_4_deg 10.07 r_rigid_bond_restr 8.076 r_dihedral_angle_1_deg 5.872 r_lrange_it 4.249 r_lrange_other 4.051 r_scangle_it 3.559 r_scangle_other 3.55 r_scbond_it 2.963 r_scbond_other 2.937 r_mcangle_it 2.437 r_mcangle_other 2.436 r_mcbond_other 2.264 r_mcbond_it 2.258 r_angle_refined_deg 1.976 r_angle_other_deg 1.199 r_symmetry_xyhbond_nbd_refined 0.366 r_xyhbond_nbd_refined 0.258 r_nbd_other 0.251 r_nbd_refined 0.232 r_symmetry_nbd_other 0.198 r_nbtor_refined 0.17 r_symmetry_nbd_refined 0.162 r_symmetry_nbtor_other 0.091 r_chiral_restr 0.084 r_bond_refined_d 0.015 r_gen_planes_refined 0.011 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 522 Nucleic Acid Atoms Solvent Atoms 156 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing