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Structure of a triple-helix region of human Collagen type XVII 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-F11 (0.2M NaCl, 0.1M Bis-Tris pH6.5, 25% PEG 3350)
Crystal Properties Matthews coefficient Solvent content 1.83 32.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 14.21 α = 85.905 b = 26.373 β = 88.974 c = 80.611 γ = 88.347
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 1.45 40.2 95.8 0.995 8.3 3.5 19828
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 1.45 1.47 0.899
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.45 40.198 19781 1045 95.616 0.169 0.1664 0.2117 0.2493 14.451
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] -0.18 -0.157 0.08 0.007 -0.797 0.054
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 22.612 r_dihedral_angle_3_deg 13.507 r_lrange_it 6.383 r_lrange_other 6.073 r_scangle_it 5.407 r_dihedral_angle_1_deg 5.404 r_scangle_other 5.404 r_scbond_it 3.977 r_scbond_other 3.974 r_mcangle_it 3.749
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 22.612 r_dihedral_angle_3_deg 13.507 r_lrange_it 6.383 r_lrange_other 6.073 r_scangle_it 5.407 r_dihedral_angle_1_deg 5.404 r_scangle_other 5.404 r_scbond_it 3.977 r_scbond_other 3.974 r_mcangle_it 3.749 r_mcangle_other 3.748 r_mcbond_it 2.464 r_mcbond_other 2.463 r_angle_refined_deg 1.49 r_angle_other_deg 0.492 r_nbd_refined 0.199 r_symmetry_xyhbond_nbd_refined 0.191 r_xyhbond_nbd_refined 0.189 r_symmetry_nbd_other 0.18 r_nbtor_refined 0.173 r_nbd_other 0.171 r_symmetry_nbd_refined 0.146 r_ncsr_local_group_2 0.138 r_ncsr_local_group_11 0.129 r_chiral_restr_other 0.111 r_ncsr_local_group_4 0.111 r_ncsr_local_group_10 0.108 r_ncsr_local_group_13 0.106 r_ncsr_local_group_15 0.105 r_symmetry_nbtor_other 0.098 r_ncsr_local_group_8 0.096 r_ncsr_local_group_5 0.091 r_ncsr_local_group_14 0.087 r_ncsr_local_group_12 0.086 r_ncsr_local_group_3 0.085 r_ncsr_local_group_1 0.081 r_ncsr_local_group_6 0.074 r_ncsr_local_group_9 0.074 r_chiral_restr 0.063 r_ncsr_local_group_7 0.063 r_bond_refined_d 0.01 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1143 Nucleic Acid Atoms Solvent Atoms 316 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing