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Crystal structure of the heterodimeric human C-P4H-II with truncated alpha subunit (C-P4H-II delta281)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2JIG 2JIG,4EL1,6I7S experimental model PDB 4EL1 2JIG,4EL1,6I7S experimental model PDB 6I7S 2JIG,4EL1,6I7S
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 278 20% (w/v) PEG4000, 0.2 M lithium sulfate, 0.1 M MES, 3% methanol
Crystal Properties Matthews coefficient Solvent content 2.36 47.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 252.879 α = 90 b = 252.879 β = 90 c = 89.4 γ = 120
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) Rrim I (All) 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 3.85 46.69 99.9 0.064 0.071 0.031 0.996 8.2 5.3 20176 203
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.85 3.99 100 1.862 2.058 0.873 0.7 5.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2JIG,4EL1,6I7S 3.85 46.69 20135 1992 99.7 0.2472 0.2438 0.2614 0.2778 0.2991 RANDOM 73.21
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] 48.6191 48.6191 -97.2383
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 18.8 t_omega_torsion 2.97 t_angle_deg 0.98 t_bond_d 0.008 t_dihedral_angle_d t_gen_planes t_it t_chiral_improper_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11081 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 10
Software Software Software Name Purpose BUSTER refinement XDS data reduction Aimless data scaling MOLREP phasing PHASER phasing