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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 Crystal-C4:0.2M NaAc, 0.1M Sodium cacodylate pH6.5, 30% PEG8,000
Crystal Properties Matthews coefficient Solvent content 2.03 39.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 29.316 α = 90 b = 17.717 β = 101.194 c = 65.821 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 32.28 96.4 0.998 17.9 6.7 11714
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 0.989
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 32.28 11707 531 95.661 0.192 0.1902 0.1995 0.2204 0.2331 16.157
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] -0.612 -0.395 -0.802 1.456
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 18.118 r_dihedral_angle_3_deg 10.646 r_dihedral_angle_1_deg 5.916 r_lrange_it 5.288 r_lrange_other 4.883 r_dihedral_angle_2_deg 4.277 r_mcangle_it 3.236 r_mcangle_other 3.233 r_scangle_it 3.102 r_scangle_other 3.098
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 18.118 r_dihedral_angle_3_deg 10.646 r_dihedral_angle_1_deg 5.916 r_lrange_it 5.288 r_lrange_other 4.883 r_dihedral_angle_2_deg 4.277 r_mcangle_it 3.236 r_mcangle_other 3.233 r_scangle_it 3.102 r_scangle_other 3.098 r_scbond_it 2.124 r_scbond_other 2.12 r_mcbond_it 2.037 r_mcbond_other 2.037 r_angle_refined_deg 1.849 r_angle_other_deg 0.569 r_nbd_refined 0.207 r_symmetry_xyhbond_nbd_refined 0.204 r_xyhbond_nbd_refined 0.198 r_symmetry_nbd_other 0.179 r_nbtor_refined 0.179 r_nbd_other 0.139 r_ncsr_local_group_1 0.129 r_ncsr_local_group_3 0.1 r_symmetry_nbtor_other 0.094 r_ncsr_local_group_2 0.084 r_chiral_restr 0.069 r_gen_planes_refined 0.012 r_bond_refined_d 0.011 r_chiral_restr_other 0.009 r_symmetry_nbd_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 481 Nucleic Acid Atoms Solvent Atoms 125 Heterogen Atoms 6
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing