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Glycoside hydrolase familiy 191 enzyme from Thermotoga maritima
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 292 PEG MME 2000, Tris
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 195.186 α = 90 b = 84.497 β = 119.914 c = 195.482 γ = 90
Symmetry Space Group P 1 21 1
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 2018-11-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, DESY BEAMLINE P11 1.0332 PETRA III, DESY P11
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 2.4 48.945 100 0.183 0.217 0.115 0.985 6.4 6.9 216213
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 2.4 2.44 1.933 2.277 1.194 0.412 7
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 2.4 48.945 216195 11162 99.936 0.238 0.2364 0.2375 0.2639 0.2669 53.804
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] 1.235 -0.097 -2.17 0.63
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.381 r_dihedral_angle_6_deg 15.305 r_dihedral_angle_2_deg 13.969 r_lrange_other 13.392 r_lrange_it 13.38 r_scangle_it 11.513 r_scangle_other 11.512 r_mcangle_it 9.8 r_mcangle_other 9.799 r_scbond_it 8.562
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.381 r_dihedral_angle_6_deg 15.305 r_dihedral_angle_2_deg 13.969 r_lrange_other 13.392 r_lrange_it 13.38 r_scangle_it 11.513 r_scangle_other 11.512 r_mcangle_it 9.8 r_mcangle_other 9.799 r_scbond_it 8.562 r_scbond_other 8.562 r_mcbond_it 7.355 r_mcbond_other 7.355 r_dihedral_angle_1_deg 6.875 r_angle_refined_deg 2.118 r_angle_other_deg 0.775 r_symmetry_nbd_refined 0.274 r_nbd_other 0.238 r_nbd_refined 0.225 r_xyhbond_nbd_refined 0.211 r_symmetry_nbd_other 0.209 r_nbtor_refined 0.194 r_symmetry_xyhbond_nbd_other 0.126 r_chiral_restr 0.111 r_ncsr_local_group_6 0.102 r_ncsr_local_group_10 0.102 r_ncsr_local_group_13 0.101 r_ncsr_local_group_4 0.099 r_ncsr_local_group_8 0.099 r_ncsr_local_group_3 0.096 r_ncsr_local_group_1 0.094 r_ncsr_local_group_2 0.094 r_ncsr_local_group_7 0.094 r_ncsr_local_group_12 0.092 r_ncsr_local_group_11 0.091 r_symmetry_xyhbond_nbd_refined 0.09 r_ncsr_local_group_15 0.089 r_ncsr_local_group_5 0.087 r_ncsr_local_group_14 0.087 r_symmetry_nbtor_other 0.084 r_ncsr_local_group_9 0.083 r_bond_refined_d 0.012 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 14028 Nucleic Acid Atoms Solvent Atoms 540 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement REFMAC refinement Aimless data scaling XDS data reduction MOLREP phasing