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Peptide-substrate-binding (PSB) domain of human type I 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 2V5F
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 278 30% MPD, 48 mM MgCl2, 50 mM KCl, 100 mM MOPS, 5 mM peptide (POG-PAG-POG)
Crystal Properties Matthews coefficient Solvent content 3.06 59.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.041 α = 90 b = 85.561 β = 90 c = 92.506 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 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 2.05 92.51 98.8 0.072 0.03 0.999 14.8 6.6 40436 46.01
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 2.05 2.11 97.2 1.65 0.676 0.468 1.6 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.05 62.89 40403 1965 98.52 0.198 0.1972 0.1972 0.218 0.2181 Random selection 60.834
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] 1.25 1.176 -2.426
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.276 r_dihedral_angle_3_deg 14.504 r_lrange_it 12.125 r_lrange_other 12.11 r_dihedral_angle_2_deg 10.872 r_scangle_it 9.996 r_scangle_other 9.994 r_scbond_it 6.489 r_scbond_other 6.488 r_mcangle_other 5.674
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.276 r_dihedral_angle_3_deg 14.504 r_lrange_it 12.125 r_lrange_other 12.11 r_dihedral_angle_2_deg 10.872 r_scangle_it 9.996 r_scangle_other 9.994 r_scbond_it 6.489 r_scbond_other 6.488 r_mcangle_other 5.674 r_mcangle_it 5.672 r_dihedral_angle_1_deg 4.99 r_mcbond_other 4.204 r_mcbond_it 4.203 r_angle_refined_deg 1.686 r_angle_other_deg 0.565 r_nbd_refined 0.231 r_nbtor_refined 0.191 r_symmetry_nbd_other 0.18 r_xyhbond_nbd_refined 0.173 r_nbd_other 0.151 r_symmetry_xyhbond_nbd_refined 0.147 r_symmetry_nbd_refined 0.14 r_ncsr_local_group_4 0.122 r_ncsr_local_group_6 0.121 r_ncsr_local_group_1 0.108 r_ncsr_local_group_3 0.108 r_ncsr_local_group_2 0.091 r_ncsr_local_group_5 0.085 r_chiral_restr 0.081 r_symmetry_nbtor_other 0.074 r_metal_ion_refined 0.059 r_symmetry_xyhbond_nbd_other 0.055 r_bond_refined_d 0.008 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 3466 Nucleic Acid Atoms Solvent Atoms 129 Heterogen Atoms 149
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing