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Maltodextrin phosphorylase (MalP) in complex with a alpha-1,2-cyclophellitol analogue
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1L5V
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.2-0.5 M Li2SO4 monohydrate, 0.1 M Bis-Tris pH 5.5-7.0 and 25-30% (w/v) PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.75 55.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 110.498 α = 90 b = 119.79 β = 90 c = 150.75 γ = 90
Symmetry Space Group P 21 21 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 16M 2023-05-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9763 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.89 71.503 99.9 0.992 5.9 1.9 160021
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.89 1.92 97.1 0.284 0.3
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 NONE 2.18 71.503 159923 1377 99.992 0.178 0.1773 0.1856 0.2294 0.2382 36.046
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] 2.095 -1.845 -0.25
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.369 r_dihedral_angle_6_deg 15.704 r_dihedral_angle_2_deg 12.402 r_lrange_other 8.268 r_lrange_it 8.266 r_scangle_it 7.713 r_scangle_other 7.395 r_dihedral_angle_1_deg 7.25 r_scbond_it 5.817 r_mcangle_other 5.743
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.369 r_dihedral_angle_6_deg 15.704 r_dihedral_angle_2_deg 12.402 r_lrange_other 8.268 r_lrange_it 8.266 r_scangle_it 7.713 r_scangle_other 7.395 r_dihedral_angle_1_deg 7.25 r_scbond_it 5.817 r_mcangle_other 5.743 r_mcangle_it 5.741 r_scbond_other 5.617 r_mcbond_it 4.589 r_mcbond_other 4.583 r_angle_refined_deg 2.381 r_angle_other_deg 0.842 r_symmetry_xyhbond_nbd_refined 0.288 r_nbd_refined 0.232 r_nbd_other 0.228 r_symmetry_nbd_other 0.206 r_symmetry_nbd_refined 0.202 r_nbtor_refined 0.193 r_xyhbond_nbd_refined 0.172 r_chiral_restr 0.132 r_symmetry_xyhbond_nbd_other 0.095 r_ncsr_local_group_1 0.095 r_symmetry_nbtor_other 0.09 r_bond_refined_d 0.015 r_gen_planes_refined 0.012 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12599 Nucleic Acid Atoms Solvent Atoms 630 Heterogen Atoms 312
Software Software Software Name Purpose REFMAC refinement DIALS data scaling Coot model building MOLREP phasing xia2 data reduction