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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 0.04M K phosphate monobasic, 16% w/v PEG 8000, 20% v/v Glycerol
Crystal Properties Matthews coefficient Solvent content 1.74 29.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 15.783 α = 90 b = 19.439 β = 93.77 c = 83.164 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 2022-02-18 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 1.5 41.49 97.4 0.021 48.1 6.3 8076
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 1.5 1.53 0.058
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 1.5 20.755 8070 374 96.635 0.168 0.1668 0.1729 0.1997 0.2031 21.368
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] 0.14 -0.421 -0.336 0.25
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 20.258 r_dihedral_angle_3_deg 9.334 r_dihedral_angle_1_deg 7.677 r_lrange_it 5.594 r_lrange_other 5.54 r_scangle_it 4.064 r_scangle_other 4.055 r_mcangle_it 3.719 r_mcangle_other 3.705 r_scbond_it 2.801
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 20.258 r_dihedral_angle_3_deg 9.334 r_dihedral_angle_1_deg 7.677 r_lrange_it 5.594 r_lrange_other 5.54 r_scangle_it 4.064 r_scangle_other 4.055 r_mcangle_it 3.719 r_mcangle_other 3.705 r_scbond_it 2.801 r_scbond_other 2.745 r_mcbond_it 2.254 r_mcbond_other 2.22 r_angle_refined_deg 1.694 r_angle_other_deg 1.051 r_symmetry_xyhbond_nbd_refined 0.252 r_nbd_refined 0.21 r_xyhbond_nbd_refined 0.203 r_nbd_other 0.202 r_symmetry_nbd_other 0.185 r_symmetry_nbd_refined 0.182 r_nbtor_refined 0.17 r_symmetry_nbtor_other 0.09 r_chiral_restr 0.066 r_bond_refined_d 0.013 r_gen_planes_refined 0.009 r_chiral_restr_other 0.004 r_bond_other_d 0.001 r_gen_planes_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 494 Nucleic Acid Atoms Solvent Atoms 78 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing