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Structure of a triple-helix region of human Collagen type II from Trautec
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1K6F
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 Index-G12:0.2M MgCl2, 0.1M HEPES pH7.5, 25% PEG3,350
Crystal Properties Matthews coefficient Solvent content 1.98 33.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 34.987 α = 90 b = 20.042 β = 99.984 c = 44.985 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 2024-07-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL45XU 0.99999 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 1.75 44.3 99.7 0.908 3.5 5.6 6457
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 1.75 1.78 0.812
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 1K6F 1.75 44.3 6450 299 99.737 0.243 0.2407 0.2447 0.2879 0.2841 15.135
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] 0.743 0.446 1.249 -2.023
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.645 r_dihedral_angle_3_deg 9.992 r_dihedral_angle_2_deg 6.887 r_dihedral_angle_1_deg 5.711 r_lrange_it 4.287 r_lrange_other 4.133 r_scangle_it 2.615 r_scangle_other 2.612 r_mcangle_it 2.172 r_mcangle_other 2.169
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.645 r_dihedral_angle_3_deg 9.992 r_dihedral_angle_2_deg 6.887 r_dihedral_angle_1_deg 5.711 r_lrange_it 4.287 r_lrange_other 4.133 r_scangle_it 2.615 r_scangle_other 2.612 r_mcangle_it 2.172 r_mcangle_other 2.169 r_scbond_it 1.646 r_scbond_other 1.643 r_angle_refined_deg 1.489 r_mcbond_it 1.314 r_mcbond_other 1.312 r_angle_other_deg 0.432 r_xyhbond_nbd_refined 0.195 r_nbd_refined 0.183 r_symmetry_xyhbond_nbd_refined 0.181 r_symmetry_nbd_other 0.172 r_nbtor_refined 0.164 r_nbd_other 0.149 r_symmetry_nbd_refined 0.114 r_symmetry_nbtor_other 0.089 r_chiral_restr 0.061 r_bond_refined_d 0.008 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 554 Nucleic Acid Atoms Solvent Atoms 84 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing