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Dispersin from Lactiplantibacillus paraplantarum DispLp
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1YHT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.2 M calcium chloride, 0.1 M sodium acetate pH 5.0, 20% PEG 6000 (PACT A10), MMS from Hampton D10
Crystal Properties Matthews coefficient Solvent content 2.07 40.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.902 α = 90 b = 82.792 β = 98.115 c = 80.642 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 PILATUS3 6M 2017-10-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97625 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 1.05 38.06 90.5 0.079 0.105 0.068 0.994 6.6 3.7 256432
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 1.05 1.07 1.052 1.411 0.93 0.422 2.2
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 THROUGHOUT 1.05 38.057 256370 12700 90.547 0.148 0.1474 0.1474 0.1696 0.1697 13.86
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] 1.303 0.098 0.824 -2.071
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 22.195 r_lrange_other 22.194 r_scbond_it 18.057 r_scbond_other 18.054 r_dihedral_angle_6_deg 17.104 r_scangle_it 16.871 r_scangle_other 16.871 r_dihedral_angle_3_deg 12.357 r_dihedral_angle_2_deg 9.105 r_dihedral_angle_1_deg 6.637
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 22.195 r_lrange_other 22.194 r_scbond_it 18.057 r_scbond_other 18.054 r_dihedral_angle_6_deg 17.104 r_scangle_it 16.871 r_scangle_other 16.871 r_dihedral_angle_3_deg 12.357 r_dihedral_angle_2_deg 9.105 r_dihedral_angle_1_deg 6.637 r_rigid_bond_restr 5.912 r_mcangle_other 5.242 r_mcangle_it 5.239 r_mcbond_it 3.747 r_mcbond_other 3.736 r_angle_refined_deg 1.734 r_angle_other_deg 0.688 r_nbd_refined 0.235 r_nbtor_refined 0.177 r_nbd_other 0.174 r_symmetry_nbd_other 0.17 r_symmetry_xyhbond_nbd_refined 0.163 r_xyhbond_nbd_refined 0.126 r_symmetry_nbd_refined 0.101 r_chiral_restr 0.095 r_ncsr_local_group_1 0.091 r_symmetry_nbtor_other 0.073 r_bond_refined_d 0.011 r_gen_planes_refined 0.01 r_bond_other_d 0.003 r_gen_planes_other 0.003 r_chiral_restr_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5246 Nucleic Acid Atoms Solvent Atoms 772 Heterogen Atoms 51
Software Software Software Name Purpose REFMAC refinement REFMAC refinement Aimless data scaling XDS data reduction Aimless data scaling MOLREP phasing