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Structure of a triple-helix region of human collagen type I from Trautec
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6SYJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.2M NaCl, 0.1M Bis-Tris pH5.5, 25% PEG3,350
Crystal Properties Matthews coefficient Solvent content 1.76 30.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 24.837 α = 95.535 b = 29.096 β = 90 c = 85.236 γ = 90
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 2023-06-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL45XU 1.00000 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 1.5 28.28 96.2 0.997 10.9 2.9 36638
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 1.5 1.53 0.881
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-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.5 28.28 36637 1774 96.155 0.197 0.1933 0.1954 0.2645 0.2633 27.277
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] 1.449 -0.105 0.173 0.197 0.049 -1.625
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.802 r_dihedral_angle_4_deg 21.805 r_dihedral_angle_3_deg 14.533 r_dihedral_angle_1_deg 5.423 r_lrange_it 3.845 r_lrange_other 3.804 r_scangle_it 3.509 r_scangle_other 3.444 r_mcangle_it 3.199 r_mcangle_other 3.193
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.802 r_dihedral_angle_4_deg 21.805 r_dihedral_angle_3_deg 14.533 r_dihedral_angle_1_deg 5.423 r_lrange_it 3.845 r_lrange_other 3.804 r_scangle_it 3.509 r_scangle_other 3.444 r_mcangle_it 3.199 r_mcangle_other 3.193 r_scbond_it 2.925 r_scbond_other 2.85 r_mcbond_it 2.752 r_mcbond_other 2.747 r_rigid_bond_restr 1.912 r_angle_refined_deg 1.473 r_angle_other_deg 1.178 r_nbd_other 0.242 r_symmetry_nbd_other 0.205 r_symmetry_xyhbond_nbd_refined 0.203 r_xyhbond_nbd_refined 0.198 r_nbd_refined 0.194 r_nbtor_refined 0.162 r_symmetry_nbd_refined 0.156 r_symmetry_xyhbond_nbd_other 0.149 r_ncsr_local_group_54 0.133 r_ncsr_local_group_49 0.132 r_ncsr_local_group_5 0.13 r_ncsr_local_group_19 0.129 r_ncsr_local_group_61 0.128 r_ncsr_local_group_28 0.127 r_ncsr_local_group_65 0.121 r_ncsr_local_group_36 0.118 r_ncsr_local_group_46 0.118 r_ncsr_local_group_64 0.118 r_ncsr_local_group_58 0.116 r_ncsr_local_group_2 0.115 r_ncsr_local_group_7 0.113 r_ncsr_local_group_24 0.113 r_ncsr_local_group_43 0.112 r_ncsr_local_group_4 0.111 r_ncsr_local_group_9 0.109 r_ncsr_local_group_6 0.107 r_ncsr_local_group_25 0.106 r_ncsr_local_group_15 0.103 r_ncsr_local_group_31 0.103 r_ncsr_local_group_45 0.102 r_ncsr_local_group_23 0.101 r_ncsr_local_group_11 0.1 r_ncsr_local_group_34 0.1 r_ncsr_local_group_40 0.1 r_ncsr_local_group_29 0.099 r_ncsr_local_group_32 0.098 r_ncsr_local_group_38 0.098 r_ncsr_local_group_55 0.098 r_ncsr_local_group_26 0.097 r_ncsr_local_group_44 0.096 r_ncsr_local_group_50 0.096 r_ncsr_local_group_53 0.096 r_ncsr_local_group_63 0.096 r_ncsr_local_group_66 0.096 r_ncsr_local_group_59 0.095 r_ncsr_local_group_62 0.095 r_ncsr_local_group_10 0.094 r_ncsr_local_group_21 0.094 r_ncsr_local_group_42 0.094 r_ncsr_local_group_60 0.093 r_ncsr_local_group_57 0.092 r_ncsr_local_group_8 0.091 r_ncsr_local_group_51 0.091 r_ncsr_local_group_52 0.091 r_symmetry_nbtor_other 0.089 r_ncsr_local_group_1 0.089 r_ncsr_local_group_56 0.088 r_ncsr_local_group_12 0.087 r_ncsr_local_group_35 0.087 r_ncsr_local_group_18 0.085 r_ncsr_local_group_37 0.085 r_ncsr_local_group_39 0.085 r_ncsr_local_group_47 0.085 r_ncsr_local_group_14 0.084 r_ncsr_local_group_16 0.082 r_ncsr_local_group_17 0.082 r_ncsr_local_group_22 0.082 r_ncsr_local_group_33 0.082 r_ncsr_local_group_13 0.078 r_ncsr_local_group_27 0.077 r_ncsr_local_group_3 0.076 r_ncsr_local_group_30 0.068 r_ncsr_local_group_48 0.068 r_chiral_restr 0.063 r_ncsr_local_group_41 0.047 r_ncsr_local_group_20 0.031 r_chiral_restr_other 0.024 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2282 Nucleic Acid Atoms Solvent Atoms 246 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing