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The Crystal Structure of Alpha-Beta-fold_hydrolase from Microlunatus sagamiharensis.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.1M Bis-Tris pH6.1, 1.8M (NH4)2SO4 + 0.25% 1,3,5-Pentanetricarboxylic acid, 0.25% 4-Hydroxyphenylacetic acid, 0.25% Benzoic acid, 0.25% Poly(3-hydroxybutyric acid),0.02 M HEPES Na pH6.8
Crystal Properties Matthews coefficient Solvent content 2.59 52.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 125.212 α = 90 b = 125.212 β = 90 c = 79.73 γ = 90
Symmetry Space Group P 41 21 2
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 9M 2023-08-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08ID-1 0.953729 CLSI 08ID-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.9 49.288 100 0.131 21.6 25.2 50439
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 1.94 0.986
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 1.9 49.288 50377 2527 99.988 0.146 0.144 0.1564 0.1794 0.1924 23.733
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] 0.437 0.437 -0.873
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.277 r_dihedral_angle_4_deg 15.664 r_dihedral_angle_3_deg 12.062 r_lrange_it 6.524 r_lrange_other 6.316 r_dihedral_angle_1_deg 6.27 r_scangle_it 5.213 r_scangle_other 5.212 r_scbond_it 3.516 r_scbond_other 3.515
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.277 r_dihedral_angle_4_deg 15.664 r_dihedral_angle_3_deg 12.062 r_lrange_it 6.524 r_lrange_other 6.316 r_dihedral_angle_1_deg 6.27 r_scangle_it 5.213 r_scangle_other 5.212 r_scbond_it 3.516 r_scbond_other 3.515 r_mcangle_other 2.871 r_mcangle_it 2.868 r_mcbond_it 2.14 r_mcbond_other 2.132 r_angle_refined_deg 1.636 r_angle_other_deg 1.511 r_symmetry_xyhbond_nbd_other 0.219 r_nbd_refined 0.216 r_symmetry_xyhbond_nbd_refined 0.19 r_symmetry_nbd_other 0.177 r_nbtor_refined 0.163 r_xyhbond_nbd_refined 0.162 r_nbd_other 0.129 r_symmetry_nbd_refined 0.113 r_ncsr_local_group_1 0.104 r_chiral_restr 0.082 r_symmetry_nbtor_other 0.082 r_bond_refined_d 0.012 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4248 Nucleic Acid Atoms Solvent Atoms 634 Heterogen Atoms 88
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing