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Structural and kinetic characterization of Porphyromonas gingivalis glutaminyl cyclase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7CJE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 287.15 Purified PgQC was concentrated up to 50 mg/ml and it was mixed in a 1:0.7 volume ratio with the crystallization buffer 0.1 M TRIS pH 8.0, 0.3 M MgNO3(H2O)6, 24% (w/v) PEG8000) incubating at 14 C
Crystal Properties Matthews coefficient Solvent content 2.7 54.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.117 α = 90 b = 91.117 β = 90 c = 165.063 γ = 120
Symmetry Space Group P 31 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 150 PIXEL Bruker PHOTON II 2020-06-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SEALED TUBE BRUKER IMUS MICROFOCUS 1.54184
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 45.56 99.9 0.2057 27.83 24 103509 31.75
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.07 100 1.565 1.76 15.1
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 7CJE 2 32.06 1.358 103501 5166 99.9 0.18 0.179 0.1801 0.215 0.2158 RANDOM 48.83
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 12.873 f_angle_d 0.576 f_chiral_restr 0.043 f_bond_d 0.003 f_plane_restr 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4385 Nucleic Acid Atoms Solvent Atoms 333 Heterogen Atoms 49
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PHASER phasing