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Peptide-substrate-binding (PSB) domain of human type I collagen prolyl 4-hydroxylase complexed with Pro-Pro-Gly-Pro-Arg-Gly-Pro-Pro-Gly.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1TJC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 278 30% MPD, 50 mM MgCl2, 50 mM KCl, 100 mM MOPS
Crystal Properties Matthews coefficient Solvent content 2.73 55.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.418 α = 90 b = 86.315 β = 90 c = 91.132 γ = 90
Symmetry Space Group P 21 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 CRL 2017-09-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-1 0.966 ESRF MASSIF-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.17 49.88 99.6 0.058 0.999 13.5 4.7 34940 52.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.17 2.25 99.6 1.412 0.482 1.1 4.7
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.17 49.88 34846 1726 99.387 0.226 0.225 0.2277 0.2499 0.2521 Random selection 63.77
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] -0.606 -1.1 1.706
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.629 r_dihedral_angle_3_deg 15.195 r_dihedral_angle_2_deg 13.461 r_lrange_it 9.373 r_lrange_other 9.372 r_scangle_it 6.239 r_scangle_other 6.238 r_dihedral_angle_1_deg 4.942 r_scbond_it 4.046 r_scbond_other 4.033
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.629 r_dihedral_angle_3_deg 15.195 r_dihedral_angle_2_deg 13.461 r_lrange_it 9.373 r_lrange_other 9.372 r_scangle_it 6.239 r_scangle_other 6.238 r_dihedral_angle_1_deg 4.942 r_scbond_it 4.046 r_scbond_other 4.033 r_mcangle_it 3.656 r_mcangle_other 3.655 r_mcbond_it 2.432 r_mcbond_other 2.432 r_angle_refined_deg 1.525 r_angle_other_deg 0.522 r_nbd_refined 0.222 r_nbtor_refined 0.185 r_nbd_other 0.184 r_xyhbond_nbd_refined 0.181 r_symmetry_xyhbond_nbd_refined 0.178 r_symmetry_nbd_other 0.175 r_symmetry_nbd_refined 0.138 r_ncsr_local_group_6 0.112 r_ncsr_local_group_4 0.104 r_ncsr_local_group_2 0.098 r_ncsr_local_group_3 0.093 r_ncsr_local_group_1 0.092 r_ncsr_local_group_5 0.09 r_metal_ion_refined 0.078 r_chiral_restr 0.073 r_symmetry_nbtor_other 0.071 r_bond_refined_d 0.007 r_gen_planes_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 3453 Nucleic Acid Atoms Solvent Atoms 130 Heterogen Atoms 149
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing