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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 Crystal-C7:0.2M (NH4)2SO4, 30% PEG4,000
Crystal Properties Matthews coefficient Solvent content 1.88 34.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.777 α = 90 b = 14.204 β = 105.826 c = 48.46 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 2024-06-25 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 1.45 46.62 97.8 0.999 16.7 6.6 11458
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 0.826
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 1.45 46.62 11457 578 97.957 0.185 0.1831 0.1913 0.2235 0.2335 24.276
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] -1.422 0.234 -1.549 2.446
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 17.73 r_dihedral_angle_6_deg 17.482 r_lrange_other 15.913 r_scangle_it 12.153 r_scangle_other 11.871 r_dihedral_angle_3_deg 11.766 r_mcangle_other 10.293 r_mcangle_it 10.283 r_scbond_it 8.533 r_scbond_other 8.192
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 17.73 r_dihedral_angle_6_deg 17.482 r_lrange_other 15.913 r_scangle_it 12.153 r_scangle_other 11.871 r_dihedral_angle_3_deg 11.766 r_mcangle_other 10.293 r_mcangle_it 10.283 r_scbond_it 8.533 r_scbond_other 8.192 r_dihedral_angle_2_deg 8.089 r_mcbond_it 7.173 r_mcbond_other 7.129 r_dihedral_angle_1_deg 5.837 r_rigid_bond_restr 4.489 r_angle_refined_deg 1.951 r_angle_other_deg 0.678 r_symmetry_xyhbond_nbd_other 0.428 r_symmetry_xyhbond_nbd_refined 0.301 r_xyhbond_nbd_refined 0.291 r_nbd_refined 0.218 r_nbd_other 0.206 r_symmetry_nbd_refined 0.201 r_symmetry_nbd_other 0.182 r_nbtor_refined 0.182 r_symmetry_nbtor_other 0.091 r_chiral_restr 0.08 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 575 Nucleic Acid Atoms Solvent Atoms 95 Heterogen Atoms 5
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing