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Glycoside hydrolase family 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 282 PEG MME 2000, Tris
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 196.055 α = 90 b = 84.499 β = 119.828 c = 196.634 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 2019-07-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.91840 BESSY 14.1
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 2.6 49.262 99.5 0.194 0.255 0.164 0.978 5.4 4.3 171234
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 2.6 2.64 1.089 1.433 0.922 0.36 4.4
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 2.6 49.262 171220 8591 99.325 0.218 0.2164 0.2179 0.2436 0.2453 40.519
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] -1.153 -0.965 -0.477 1.651
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.029 r_dihedral_angle_6_deg 15.135 r_dihedral_angle_2_deg 11.389 r_lrange_it 11.363 r_lrange_other 11.354 r_scangle_it 9.654 r_scangle_other 9.654 r_mcangle_other 7.99 r_mcangle_it 7.989 r_dihedral_angle_1_deg 7.43
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.029 r_dihedral_angle_6_deg 15.135 r_dihedral_angle_2_deg 11.389 r_lrange_it 11.363 r_lrange_other 11.354 r_scangle_it 9.654 r_scangle_other 9.654 r_mcangle_other 7.99 r_mcangle_it 7.989 r_dihedral_angle_1_deg 7.43 r_scbond_it 6.675 r_scbond_other 6.675 r_mcbond_it 5.595 r_mcbond_other 5.595 r_angle_refined_deg 2.358 r_angle_other_deg 0.797 r_symmetry_nbd_refined 0.255 r_nbd_other 0.242 r_nbd_refined 0.221 r_xyhbond_nbd_refined 0.211 r_symmetry_nbd_other 0.203 r_symmetry_xyhbond_nbd_refined 0.202 r_nbtor_refined 0.195 r_chiral_restr 0.109 r_symmetry_xyhbond_nbd_other 0.095 r_symmetry_nbtor_other 0.092 r_ncsr_local_group_3 0.065 r_ncsr_local_group_13 0.065 r_ncsr_local_group_15 0.064 r_ncsr_local_group_1 0.063 r_ncsr_local_group_4 0.063 r_ncsr_local_group_10 0.063 r_ncsr_local_group_2 0.062 r_ncsr_local_group_5 0.062 r_ncsr_local_group_6 0.062 r_ncsr_local_group_8 0.06 r_ncsr_local_group_11 0.06 r_ncsr_local_group_7 0.059 r_ncsr_local_group_9 0.057 r_ncsr_local_group_14 0.057 r_ncsr_local_group_12 0.056 r_bond_refined_d 0.013 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 14037 Nucleic Acid Atoms Solvent Atoms 596 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement REFMAC refinement Aimless data scaling XDS data reduction MOLREP phasing