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Crystal structure of the metalloproteinase enhancer PCPE-1 bound to the procollagen C propeptide trimer (short)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4AE2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 295 20 mg/ml protein in 20 mM HEPES pH 7.5, 180 mM NaCl, 2.5 mM calcium chloride; 0.2 M potassium citrate, 16% PEG3350
Crystal Properties Matthews coefficient Solvent content 4.43 72.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.09 α = 90 b = 144.12 β = 90 c = 158.74 γ = 90
Symmetry Space Group P 21 21 21
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 PILATUS 6M 2016-04-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.9282 Diamond I04-1
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 2.7 79.4 99.9 0.087 0.998 17.1 13.1 56733
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 2.7 2.77 99.9 1.94 0.743 1.2 13.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 4AE2 2.7 79.37 1.34 56733 2827 99.77 0.2275 0.2259 0.2363 0.258 0.26
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 12.547 f_angle_d 0.737 f_chiral_restr 0.031 f_bond_d 0.003 f_plane_restr 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7361 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 46
Software Software Software Name Purpose PHENIX refinement xia2 data reduction xia2 data scaling PHASER phasing