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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-H6 (0.2M Sodium formate, 20% PEG 3350)
Crystal Properties Matthews coefficient Solvent content 1.84 33.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 33.96 α = 90 b = 13.757 β = 100.116 c = 66.084 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 1.45 32.53 98.7 0.998 15.2 6.5 11135
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 0.634
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 1.45 32.53 11131 1134 98.644 0.237 0.2303 0.2283 0.2984 0.3094 25.61
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] -0.592 -4.467 -0.022 2.075
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 20.893 r_lrange_it 15.026 r_lrange_other 14.309 r_dihedral_angle_3_deg 9.134 r_scangle_it 9.112 r_scangle_other 9.101 r_mcangle_it 9.021 r_mcangle_other 9.021 r_mcbond_it 6.331 r_scbond_it 6.312
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 20.893 r_lrange_it 15.026 r_lrange_other 14.309 r_dihedral_angle_3_deg 9.134 r_scangle_it 9.112 r_scangle_other 9.101 r_mcangle_it 9.021 r_mcangle_other 9.021 r_mcbond_it 6.331 r_scbond_it 6.312 r_scbond_other 6.299 r_mcbond_other 6.289 r_dihedral_angle_1_deg 5.503 r_rigid_bond_restr 4.682 r_angle_refined_deg 1.573 r_angle_other_deg 0.527 r_symmetry_nbd_refined 0.256 r_nbd_other 0.206 r_nbd_refined 0.205 r_symmetry_nbd_other 0.18 r_nbtor_refined 0.168 r_xyhbond_nbd_refined 0.158 r_symmetry_xyhbond_nbd_refined 0.158 r_symmetry_nbtor_other 0.083 r_chiral_restr 0.07 r_chiral_restr_other 0.017 r_bond_refined_d 0.008 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 548 Nucleic Acid Atoms Solvent Atoms 61 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing