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Ruminococcus gnavus GH29 fucosidase E1_10125 D221A mutant in complex with fucose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4OUE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 273 2 M magnesium chloride, 25% PEG 3350, 0.1 M bis-tris pH 5.5, 10mM 2FL
Crystal Properties Matthews coefficient Solvent content 2.12 41.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.78 α = 82.47 b = 74.06 β = 80.43 c = 76.509 γ = 70.41
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 2018-09-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9763 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 1.45 69.64 92.7 0.043 0.06 0.043 0.995 12.7 2 166349
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 1.45 1.47 56.9 0.111 0.157 0.111 0.955 1.8
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 (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 4OUE 1.45 69.64 158233 8116 92.66 0.1416 0.1406 0.1497 0.1605 0.169 RANDOM 11.7
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] 0.33 -0.02 0.07 -0.51 -0.04 0.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.7 r_dihedral_angle_4_deg 14.34 r_dihedral_angle_3_deg 11.687 r_dihedral_angle_1_deg 6.295 r_angle_other_deg 1.712 r_angle_refined_deg 1.432 r_chiral_restr 0.069 r_bond_other_d 0.019 r_bond_refined_d 0.009 r_gen_planes_refined 0.007
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.7 r_dihedral_angle_4_deg 14.34 r_dihedral_angle_3_deg 11.687 r_dihedral_angle_1_deg 6.295 r_angle_other_deg 1.712 r_angle_refined_deg 1.432 r_chiral_restr 0.069 r_bond_other_d 0.019 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_gen_planes_other 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7962 Nucleic Acid Atoms Solvent Atoms 1507 Heterogen Atoms 48
Software Software Software Name Purpose Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction xia2 data reduction PHASER phasing