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Structure of a triple-helix region of human Collagen type IV 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-D5:0.1M NaAc pH4.5, 25% PEG3,350
Crystal Properties Matthews coefficient Solvent content 1.76 30.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 13.982 α = 86.62 b = 30.428 β = 86.473 c = 68.051 γ = 89.284
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 33.9 95.6 0.992 11.1 3.4 18950
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 1.48 0.98
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 33.9 18949 801 95.591 0.164 0.1615 0.1684 0.2106 0.2098 15.735
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] 0.089 0.409 -0.543 -1.283 0.194 1.145
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 18.34 r_dihedral_angle_3_deg 10.527 r_dihedral_angle_1_deg 5.861 r_dihedral_angle_2_deg 5.522 r_lrange_it 4.827 r_lrange_other 4.56 r_scangle_it 3.201 r_scangle_other 3.199 r_mcangle_it 2.703 r_mcangle_other 2.702
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 18.34 r_dihedral_angle_3_deg 10.527 r_dihedral_angle_1_deg 5.861 r_dihedral_angle_2_deg 5.522 r_lrange_it 4.827 r_lrange_other 4.56 r_scangle_it 3.201 r_scangle_other 3.199 r_mcangle_it 2.703 r_mcangle_other 2.702 r_scbond_it 2.155 r_scbond_other 2.153 r_mcbond_it 1.821 r_mcbond_other 1.817 r_angle_refined_deg 1.645 r_angle_other_deg 0.55 r_symmetry_xyhbond_nbd_refined 0.237 r_nbd_refined 0.194 r_symmetry_nbd_refined 0.194 r_symmetry_nbd_other 0.18 r_nbtor_refined 0.178 r_xyhbond_nbd_refined 0.167 r_nbd_other 0.152 r_ncsr_local_group_4 0.144 r_ncsr_local_group_1 0.141 r_ncsr_local_group_10 0.138 r_ncsr_local_group_2 0.131 r_ncsr_local_group_15 0.129 r_ncsr_local_group_13 0.122 r_ncsr_local_group_11 0.121 r_ncsr_local_group_5 0.12 r_ncsr_local_group_14 0.12 r_ncsr_local_group_6 0.118 r_ncsr_local_group_9 0.108 r_ncsr_local_group_8 0.104 r_ncsr_local_group_7 0.1 r_ncsr_local_group_12 0.095 r_ncsr_local_group_3 0.093 r_symmetry_nbtor_other 0.091 r_chiral_restr 0.071 r_chiral_restr_other 0.06 r_bond_refined_d 0.012 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1117 Nucleic Acid Atoms Solvent Atoms 252 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing