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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 2D3H
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.2 M Potassium chloride, 0.05 M HEPES pH 7.5, 35% PEG 400
Crystal Properties Matthews coefficient Solvent content 1.75 29.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36.936 α = 90 b = 24.334 β = 104.851 c = 60.814 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 2023-06-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL45XU 1.00000 SPring-8 BL45XU
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 35.7 99.6 0.998 14.9 5.1 18895
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 0.959 4.9
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 35.7 18887 884 99.557 0.176 0.1728 0.1732 0.2423 0.2443 20.587
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] -1.065 0.47 2.002 -1.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 13.802 r_dihedral_angle_3_deg 10.941 r_lrange_it 6.148 r_lrange_other 5.474 r_scangle_it 4.383 r_scangle_other 4.381 r_mcangle_it 4.171 r_mcangle_other 4.169 r_dihedral_angle_1_deg 4.124 r_scbond_it 3.439
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 13.802 r_dihedral_angle_3_deg 10.941 r_lrange_it 6.148 r_lrange_other 5.474 r_scangle_it 4.383 r_scangle_other 4.381 r_mcangle_it 4.171 r_mcangle_other 4.169 r_dihedral_angle_1_deg 4.124 r_scbond_it 3.439 r_mcbond_it 3.438 r_scbond_other 3.424 r_mcbond_other 3.384 r_rigid_bond_restr 2.341 r_angle_refined_deg 1.133 r_angle_other_deg 0.449 r_symmetry_nbd_refined 0.275 r_nbd_other 0.226 r_symmetry_xyhbond_nbd_refined 0.194 r_nbd_refined 0.188 r_symmetry_nbd_other 0.177 r_nbtor_refined 0.17 r_xyhbond_nbd_refined 0.142 r_symmetry_nbtor_other 0.097 r_chiral_restr 0.046 r_chiral_restr_other 0.035 r_bond_refined_d 0.007 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1034 Nucleic Acid Atoms Solvent Atoms 206 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing