☰ Navigation Tabs
Structural and kinetic characterization of Porphyromonas gingivalis glutaminyl cyclase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3GUX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 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 and using the hanging drop vapor diffusion technique.
Crystal Properties Matthews coefficient Solvent content 2.78 55.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.8 α = 90 b = 90.8 β = 90 c = 164.5 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 120 PIXEL DECTRIS PILATUS3 S 6M 2018-12-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL18U1 0.97853 SSRF BL18U1
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 1.95 19.98 99.86 0.3065 0.3106 0.04962 0.987 14.94 39.8 110402 38.2277098776
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 2.072 100 2.402 2.432 0.3814 0.701 1.45 40.5
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 3GUX 1.950006936 19.8935993803 1.37863167132 110402 3829 99.919450453 0.183418915358 0.182509299419 0.1833 0.209187450181 0.2092 RANDOM 47.1182954709
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 17.7552993799 f_angle_d 1.36851888016 f_chiral_restr 0.0892658813886 f_bond_d 0.0173009639355 f_plane_restr 0.00867939823428
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4476 Nucleic Acid Atoms Solvent Atoms 311 Heterogen Atoms 10
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling BALBES phasing