☰ Navigation Tabs
Plant/insect N-glycan active PNGase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4R4Z
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 10 mM Cobalt chloride hexahydrate, 100 mM Tris pH 8.5 and 10% w/v Polyvinylpyrrolidone K15
Crystal Properties Matthews coefficient Solvent content 2.16 42.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.05 α = 90 b = 100.55 β = 90 c = 180.37 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 2017-05-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97949 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.95 45.09 99.9 0.999 12.6 7.2 79080
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.95 1.99 99.6 0.517 1.7 7.2
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT NONE 4r4z 1.95 44.379 79007 3990 99.77 0.192 0.1892 0.1892 0.2395 0.2397 45.568
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] 0.568 -0.597 0.029
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.292 r_dihedral_angle_6_deg 16.837 r_dihedral_angle_3_deg 16.535 r_lrange_it 10.792 r_lrange_other 10.791 r_scangle_it 8.874 r_scangle_other 8.873 r_dihedral_angle_1_deg 8.089 r_mcangle_it 7.213 r_mcangle_other 7.213
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.292 r_dihedral_angle_6_deg 16.837 r_dihedral_angle_3_deg 16.535 r_lrange_it 10.792 r_lrange_other 10.791 r_scangle_it 8.874 r_scangle_other 8.873 r_dihedral_angle_1_deg 8.089 r_mcangle_it 7.213 r_mcangle_other 7.213 r_scbond_it 6.365 r_scbond_other 6.365 r_mcbond_it 5.668 r_mcbond_other 5.667 r_angle_refined_deg 1.768 r_angle_other_deg 0.577 r_nbd_refined 0.208 r_symmetry_xyhbond_nbd_refined 0.201 r_symmetry_nbd_other 0.2 r_nbd_other 0.189 r_nbtor_refined 0.185 r_xyhbond_nbd_refined 0.173 r_symmetry_nbd_refined 0.151 r_ncsr_local_group_1 0.105 r_symmetry_nbtor_other 0.092 r_chiral_restr 0.082 r_symmetry_xyhbond_nbd_other 0.034 r_bond_refined_d 0.011 r_gen_planes_refined 0.011 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8305 Nucleic Acid Atoms Solvent Atoms 336 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement Coot model building MolProbity model building PHASER phasing Aimless data scaling pointless data scaling xia2 data reduction XDS data reduction