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Peptide-substrate-binding (PSB) domain of human type I collagen prolyl 4-hydroxylase complexed with Pro-Pro-Gly-Pro-Ala-Gly-Pro-Pro-Gly.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2V5F
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 278 30% MPD, 50 mM MgCl2, 50 mM KCl, 100 mM MOPS
Crystal Properties Matthews coefficient Solvent content 3.1 60.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.64 α = 90 b = 84.64 β = 90 c = 90.166 γ = 90
Symmetry Space Group P 42 21 2
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 2M Vertical CRL, horizontal CRL 2022-09-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-1 0.9655 ESRF MASSIF-1
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 2.15 90.17 99.5 0.053 0.017 0.999 19.8 10.9 18422 63.3
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 2.15 2.21 96.6 2.275 0.713 0.548 1 10.9
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 2.15 59.921 18369 920 99.712 0.2 0.1977 0.1978 0.2408 0.2411 83.052
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] 0.815 0.815 -1.629
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 17.161 r_dihedral_angle_6_deg 17.152 r_dihedral_angle_3_deg 16.249 r_lrange_other 11.947 r_lrange_it 11.945 r_scangle_it 9.327 r_scangle_other 9.324 r_mcangle_it 6.787 r_mcangle_other 6.784 r_scbond_it 6.338
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 17.161 r_dihedral_angle_6_deg 17.152 r_dihedral_angle_3_deg 16.249 r_lrange_other 11.947 r_lrange_it 11.945 r_scangle_it 9.327 r_scangle_other 9.324 r_mcangle_it 6.787 r_mcangle_other 6.784 r_scbond_it 6.338 r_scbond_other 6.335 r_dihedral_angle_1_deg 6.235 r_mcbond_it 4.83 r_mcbond_other 4.796 r_angle_refined_deg 1.625 r_angle_other_deg 0.621 r_nbd_refined 0.21 r_nbtor_refined 0.178 r_nbd_other 0.17 r_symmetry_xyhbond_nbd_refined 0.168 r_symmetry_nbd_other 0.161 r_xyhbond_nbd_refined 0.129 r_symmetry_nbd_refined 0.129 r_ncsr_local_group_1 0.117 r_chiral_restr 0.09 r_symmetry_nbtor_other 0.07 r_metal_ion_refined 0.02 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1742 Nucleic Acid Atoms Solvent Atoms 37 Heterogen Atoms 85
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction Aimless data scaling PHASER phasing