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Crystal structure of a circular permutation and computationally designed pro-enzyme of carboxypeptidase G2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1CG2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293 Protein was prepared to a concentration of 19 mg/mL in 50 mM Tris 100 mM NaCl pH 7.4 0.2 mM ZnSO4. Reservoirs containing 750 uL of 20 mM Tris pH 8.0, 10% glycerol, and 10% PEG 3350 were prepared in 24 well hanging drop vapor diffusion plates. Equal volumes of protein solution and reservoir solution were mixed on a cover slip and suspended over the reservoir
Crystal Properties Matthews coefficient Solvent content 2.57 52.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.54 α = 90 b = 106.36 β = 107.48 c = 121.93 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 93 IMAGE PLATE RIGAKU RAXIS IV++ 2017-06-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 1.54178
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 2.59 39.27 97.2 0.102 0.125 0.071 0.952 6.8 2.9 57919
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.59 2.63 95.77 0.946 1.195 0.719 0.388 0.9 2.48
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 1CG2 2.59 39.27 45894 2346 80.89 0.22451 0.22172 0.2246 0.27917 0.2811 Random 53.598
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] 5.5 1.54 -1.71 -3.97
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10948 Nucleic Acid Atoms Solvent Atoms 132 Heterogen Atoms 25
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling PHASER phasing