☰ Navigation Tabs
GH191 family Alpha-Galactosaminidase from Environmental sample (99.2% identity to Myxococcus fulvus enzyme)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2AAM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 1.6% Ammonium Sulphate, 3% PEG 1K,10% glycerol, 24 well format Linbro plate
Crystal Properties Matthews coefficient Solvent content 1.9 35.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.84 α = 90 b = 185.324 β = 90 c = 128.391 γ = 90
Symmetry Space Group C 2 2 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 EIGER X 9M 2020-02-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.9119 Diamond I04-1
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 1.64 46.33 100 0.162 0.175 0.067 0.998 11.5 13.1 61821 14.6
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 1.64 1.67 100 3.203 3.466 1.313 0.467 0.8 13.3
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 1.64 46.33 61781 3200 99.989 0.199 0.1966 0.1964 0.2405 0.2405 20.374
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] 1.469 0.567 -2.035
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.863 r_dihedral_angle_3_deg 11.163 r_dihedral_angle_2_deg 6.37 r_dihedral_angle_1_deg 6.196 r_lrange_other 4.965 r_lrange_it 4.963 r_scangle_it 3.095 r_scangle_other 3.093 r_mcangle_it 2.161 r_mcangle_other 2.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.863 r_dihedral_angle_3_deg 11.163 r_dihedral_angle_2_deg 6.37 r_dihedral_angle_1_deg 6.196 r_lrange_other 4.965 r_lrange_it 4.963 r_scangle_it 3.095 r_scangle_other 3.093 r_mcangle_it 2.161 r_mcangle_other 2.16 r_scbond_it 2.037 r_scbond_other 2.035 r_mcbond_it 1.542 r_mcbond_other 1.541 r_angle_refined_deg 1.45 r_angle_other_deg 0.543 r_nbd_refined 0.21 r_symmetry_nbd_refined 0.202 r_nbtor_refined 0.184 r_symmetry_nbd_other 0.182 r_symmetry_xyhbond_nbd_refined 0.148 r_nbd_other 0.144 r_xyhbond_nbd_refined 0.136 r_chiral_restr 0.078 r_symmetry_nbtor_other 0.078 r_ncsr_local_group_1 0.077 r_bond_refined_d 0.008 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4231 Nucleic Acid Atoms Solvent Atoms 464 Heterogen Atoms 10
Software Software Software Name Purpose xia2 data reduction XDS data reduction Aimless data scaling MOLREP phasing REFMAC refinement