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CjGH35 with a Galactosidase Activity-Based Probe
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4D1I
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.4 291 Sodium acetate
Crystal Properties Matthews coefficient Solvent content 2.71 54.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 99.316 α = 90.236 b = 116.212 β = 89.889 c = 116.396 γ = 90.094
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 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) 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 1.5 99.32 96.3 0.043 0.061 0.043 0.997 10.4 3.4 802827
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 1.5 1.53 90 0.0467 0.66 0.0467 0.719 2 2.8
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 1.5 82.544 762488 40267 96.256 0.158 0.1566 0.1561 0.181 0.1803 21.647
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] 1.202 -0.143 0.182 -0.43 0.126 -0.771
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.172 r_dihedral_angle_3_deg 13.821 r_dihedral_angle_2_deg 7.986 r_dihedral_angle_1_deg 7.094 r_lrange_it 5.095 r_lrange_other 4.903 r_scangle_it 4.093 r_scangle_other 4.093 r_scbond_it 2.861 r_scbond_other 2.861
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.172 r_dihedral_angle_3_deg 13.821 r_dihedral_angle_2_deg 7.986 r_dihedral_angle_1_deg 7.094 r_lrange_it 5.095 r_lrange_other 4.903 r_scangle_it 4.093 r_scangle_other 4.093 r_scbond_it 2.861 r_scbond_other 2.861 r_mcangle_it 2.636 r_mcangle_other 2.636 r_mcbond_it 1.976 r_mcbond_other 1.974 r_angle_refined_deg 1.709 r_angle_other_deg 0.568 r_nbd_other 0.306 r_nbd_refined 0.228 r_symmetry_xyhbond_nbd_refined 0.21 r_symmetry_nbd_refined 0.189 r_nbtor_refined 0.185 r_symmetry_nbd_other 0.182 r_xyhbond_nbd_refined 0.174 r_metal_ion_refined 0.115 r_symmetry_metal_ion_refined 0.101 r_chiral_restr 0.089 r_symmetry_nbtor_other 0.08 r_symmetry_xyhbond_nbd_other 0.029 r_bond_refined_d 0.011 r_gen_planes_refined 0.011 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 33749 Nucleic Acid Atoms Solvent Atoms 4413 Heterogen Atoms 187
Software Software Software Name Purpose REFMAC refinement REFMAC refinement Aimless data scaling REFMAC phasing