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Structure of a triple-helix region of human Collagen type VII 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 Crystal-B6 (0.2M MgAc2, 0.1M Sodium cacodylate pH6.5, 20% PEG 8000)
Crystal Properties Matthews coefficient Solvent content 1.84 33.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 20.927 α = 78.396 b = 30.425 β = 81.644 c = 53.078 γ = 72.831
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 2024-04-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL18U1 0.97853 SSRF BL18U1
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 28.66 96.6 0.999 15.3 3.4 11871
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 0.99
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.75 28.659 11870 555 96.614 0.136 0.1331 0.1928 0.222 13.123
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] 0.103 -0.7 -0.644 0.225 0.262 -0.776
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 17.509 r_dihedral_angle_4_deg 15.357 r_dihedral_angle_3_deg 10.187 r_dihedral_angle_1_deg 5.859 r_lrange_it 4.195 r_lrange_other 3.896 r_angle_refined_deg 1.798 r_scangle_it 1.695 r_scangle_other 1.694 r_mcangle_it 1.611
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 17.509 r_dihedral_angle_4_deg 15.357 r_dihedral_angle_3_deg 10.187 r_dihedral_angle_1_deg 5.859 r_lrange_it 4.195 r_lrange_other 3.896 r_angle_refined_deg 1.798 r_scangle_it 1.695 r_scangle_other 1.694 r_mcangle_it 1.611 r_mcangle_other 1.611 r_angle_other_deg 1.204 r_scbond_it 1.063 r_scbond_other 1.062 r_mcbond_it 0.956 r_mcbond_other 0.955 r_nbd_refined 0.197 r_nbd_other 0.194 r_xyhbond_nbd_other 0.194 r_symmetry_nbd_other 0.192 r_xyhbond_nbd_refined 0.181 r_nbtor_refined 0.167 r_symmetry_xyhbond_nbd_refined 0.163 r_ncsr_local_group_9 0.135 r_ncsr_local_group_5 0.131 r_ncsr_local_group_7 0.13 r_ncsr_local_group_2 0.128 r_ncsr_local_group_3 0.123 r_ncsr_local_group_1 0.122 r_ncsr_local_group_13 0.122 r_ncsr_local_group_15 0.122 r_symmetry_nbd_refined 0.119 r_ncsr_local_group_6 0.119 r_ncsr_local_group_12 0.119 r_ncsr_local_group_14 0.116 r_ncsr_local_group_8 0.107 r_ncsr_local_group_4 0.104 r_ncsr_local_group_10 0.104 r_ncsr_local_group_11 0.103 r_symmetry_nbtor_other 0.09 r_chiral_restr 0.069 r_bond_refined_d 0.013 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 1210 Nucleic Acid Atoms Solvent Atoms 316 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing