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Peptide-substrate-binding (PSB) domain of human type II collagen prolyl 4-hydroxylase complexed with Pro-Hyp-Gly-Pro-Ala-Gly-Pro-Hyp-Gly.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6EVL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 278 2M ammonium sulphate, 10% dioxane, 100 mM MES, 2 mM Pro-Hyp-Gly-Pro-Ala-Gly-Pro-Hyp-Gly.
Crystal Properties Matthews coefficient Solvent content 2.52 51.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.655 α = 90 b = 56.655 β = 90 c = 68.828 γ = 120
Symmetry Space Group P 32 2 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 EIGER X 16M Toroidal mirror 2018-09-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2) 0.9763 PETRA III, EMBL c/o DESY P14 (MX2)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) 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 49.06 97.1 0.063 0.026 0.998 14.2 6.6 12786 27.6
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.75 1.78 98.4 1.075 0.433 0.556 1.3 6.8
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 1.751 49.06 12783 687 96.113 0.166 0.1648 0.1648 0.1951 0.1956 39.127
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] -0.196 -0.098 -0.196 0.637
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.063 r_dihedral_angle_3_deg 12.335 r_lrange_it 9.99 r_lrange_other 9.734 r_scangle_it 8.94 r_scangle_other 8.894 r_dihedral_angle_2_deg 8.494 r_scbond_it 6.025 r_scbond_other 5.953 r_mcangle_it 5.78
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.063 r_dihedral_angle_3_deg 12.335 r_lrange_it 9.99 r_lrange_other 9.734 r_scangle_it 8.94 r_scangle_other 8.894 r_dihedral_angle_2_deg 8.494 r_scbond_it 6.025 r_scbond_other 5.953 r_mcangle_it 5.78 r_mcangle_other 5.776 r_dihedral_angle_1_deg 5.556 r_mcbond_it 4.246 r_mcbond_other 4.201 r_angle_refined_deg 1.905 r_angle_other_deg 0.741 r_nbd_refined 0.219 r_xyhbond_nbd_refined 0.189 r_nbtor_refined 0.181 r_symmetry_nbd_other 0.142 r_symmetry_xyhbond_nbd_refined 0.134 r_nbd_other 0.107 r_symmetry_nbd_refined 0.103 r_chiral_restr 0.097 r_symmetry_nbtor_other 0.071 r_bond_refined_d 0.011 r_gen_planes_refined 0.01 r_gen_planes_other 0.003 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 802 Nucleic Acid Atoms Solvent Atoms 55 Heterogen Atoms 25
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing