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Nostoc sp. 3335mg GT108 family enzyme purified in HEPES, with Bis-Tris propane and phosphate in the active site
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9QVW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 293 0.2 M NaBr, 0.1 M Bis-Tris propane pH 6.5 and 20% (w/v) PEG 3,350
Crystal Properties Matthews coefficient Solvent content 3.08 60.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 131.659 α = 90 b = 131.659 β = 90 c = 47.517 γ = 90
Symmetry Space Group P 43 21 2
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 EIGER2 XE 16M 2021-02-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.976 Diamond I03
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 1.72 47.52 99.7 0.148 0.154 0.042 0.999 8 25.1 44969
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) 1.72 1.75 99.3 3.786 3.957 1.138 0.316 0.1 23.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 FREE R-VALUE 1.72 44.694 44800 2264 99.644 0.212 0.2104 0.2177 0.2428 0.2494 42.11
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] -0.028 -0.028 0.056
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.565 r_dihedral_angle_3_deg 12.333 r_dihedral_angle_2_deg 10.784 r_lrange_it 8.546 r_lrange_other 8.541 r_dihedral_angle_1_deg 7.786 r_scangle_it 6.984 r_scangle_other 6.942 r_mcangle_it 5.384 r_mcangle_other 5.384
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.565 r_dihedral_angle_3_deg 12.333 r_dihedral_angle_2_deg 10.784 r_lrange_it 8.546 r_lrange_other 8.541 r_dihedral_angle_1_deg 7.786 r_scangle_it 6.984 r_scangle_other 6.942 r_mcangle_it 5.384 r_mcangle_other 5.384 r_scbond_it 5.334 r_scbond_other 4.888 r_mcbond_it 4.027 r_mcbond_other 4.017 r_angle_refined_deg 2.009 r_angle_other_deg 0.835 r_nbd_other 0.242 r_symmetry_nbd_refined 0.226 r_nbd_refined 0.185 r_nbtor_refined 0.175 r_symmetry_nbd_other 0.167 r_xyhbond_nbd_refined 0.166 r_symmetry_xyhbond_nbd_refined 0.119 r_chiral_restr 0.105 r_symmetry_nbtor_other 0.08 r_symmetry_xyhbond_nbd_other 0.016 r_bond_refined_d 0.011 r_bond_other_d 0.003 r_gen_planes_refined 0.001 r_gen_planes_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2356 Nucleic Acid Atoms Solvent Atoms 180 Heterogen Atoms 29
Software Software Software Name Purpose REFMAC refinement Aimless data scaling DIALS data reduction MOLREP phasing