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Dispersin from Terribacillus saccharophilus Dispts2 in complex with NAG-thiazoline
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8QB6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 MPD screen E7: 0.1 M Citric acid pH 4.0, 20% MPD
Crystal Properties Matthews coefficient Solvent content 3.02 59.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.06 α = 90 b = 90.06 β = 90 c = 98.12 γ = 120
Symmetry Space Group P 32 2 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 2018-03-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.976 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 2.17 40.93 93.1 0.09 0.099 0.04 0.999 13.3 11.6 23157
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) 2.17 2.24 76.4 4.735 5.21 2.151 0.532 0.5 11.2
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 2.17 40.926 23065 1089 92.895 0.214 0.2121 0.2122 0.2528 0.2527 59.004
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] 0.595 0.298 0.595 -1.93
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.536 r_dihedral_angle_3_deg 13.6 r_lrange_it 9.215 r_lrange_other 9.215 r_dihedral_angle_2_deg 7.533 r_dihedral_angle_1_deg 6.994 r_scangle_it 6.978 r_scangle_other 6.976 r_mcangle_it 6.432 r_mcangle_other 6.43
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.536 r_dihedral_angle_3_deg 13.6 r_lrange_it 9.215 r_lrange_other 9.215 r_dihedral_angle_2_deg 7.533 r_dihedral_angle_1_deg 6.994 r_scangle_it 6.978 r_scangle_other 6.976 r_mcangle_it 6.432 r_mcangle_other 6.43 r_mcbond_it 4.642 r_mcbond_other 4.641 r_scbond_it 4.568 r_scbond_other 4.564 r_angle_refined_deg 1.482 r_angle_other_deg 0.564 r_nbd_refined 0.207 r_nbtor_refined 0.182 r_symmetry_nbd_other 0.176 r_nbd_other 0.146 r_xyhbond_nbd_refined 0.128 r_symmetry_xyhbond_nbd_refined 0.103 r_symmetry_nbtor_other 0.074 r_chiral_restr 0.069 r_symmetry_nbd_refined 0.051 r_gen_planes_refined 0.006 r_bond_refined_d 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2631 Nucleic Acid Atoms Solvent Atoms 43 Heterogen Atoms 14
Software Software Software Name Purpose REFMAC refinement REFMAC refinement Aimless data scaling XDS data reduction Aimless data scaling MOLREP phasing