☰ Navigation Tabs
Crystal structure of PNGase Bb in complex with MUXF glycopeptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other ALPHAFOLD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 EVAPORATION 291 1M Sodium citrate tribasic,0.1M Tris base/Hydrochloric acid,
200mM Sodium Chloride
Crystal Properties Matthews coefficient Solvent content 2.22 44.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 136.72 α = 90 b = 97.89 β = 122.02 c = 96.32 γ = 90
Symmetry Space Group C 1 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 100 PIXEL DECTRIS PILATUS3 6M 2024-05-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL19U1 0.9793 SSRF BL19U1
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 2.16 37.75 99.4 0.106 0.998 10.5 6.6 57354
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 2.16 2.22 1.158 0.612
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.16 33.47 1.34 57289 1999 99.25 0.21 0.2082 0.2113 0.2606 0.2625
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 9.461 f_angle_d 1.068 f_chiral_restr 0.064 f_bond_d 0.009 f_plane_restr 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8101 Nucleic Acid Atoms Solvent Atoms 261 Heterogen Atoms 188
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing