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The crystal structure of alpha/beta fold hydrolase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5Y57
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.2 289 0.1 M Bis-Tris, pH7.2, 0.2 M Magnesium acetate, 17% PEG3350
Crystal Properties Matthews coefficient Solvent content 2.39 48.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 166.96 α = 90 b = 68.41 β = 93.575 c = 75.34 γ = 90
Symmetry Space Group C 1 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 298 PIXEL DECTRIS EIGER2 S 9M 2021-10-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL02U1 0.979 SSRF BL02U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.66 57.64 98.38 0.048 0.999 19.8 6.37 98523
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.66 1.7 0.466 0.523 0.999
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 5Y57 1.66 57.638 98506 4917 98.38 0.195 0.1936 0.2287 0.2193 27.202
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] 0.227 0.578 -0.983 0.679
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.472 r_dihedral_angle_3_deg 14.84 r_dihedral_angle_1_deg 5.379 r_rigid_bond_restr 5.374 r_lrange_it 4.26 r_lrange_other 4.25 r_scangle_it 3.753 r_scangle_other 3.753 r_dihedral_angle_2_deg 3.461 r_mcangle_it 3.322
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.472 r_dihedral_angle_3_deg 14.84 r_dihedral_angle_1_deg 5.379 r_rigid_bond_restr 5.374 r_lrange_it 4.26 r_lrange_other 4.25 r_scangle_it 3.753 r_scangle_other 3.753 r_dihedral_angle_2_deg 3.461 r_mcangle_it 3.322 r_mcangle_other 3.322 r_scbond_it 3.268 r_scbond_other 3.268 r_mcbond_it 2.732 r_mcbond_other 2.732 r_angle_refined_deg 1.478 r_angle_other_deg 0.449 r_symmetry_nbd_refined 0.238 r_nbd_refined 0.229 r_symmetry_nbd_other 0.191 r_nbtor_refined 0.179 r_nbd_other 0.129 r_symmetry_xyhbond_nbd_refined 0.122 r_xyhbond_nbd_refined 0.109 r_symmetry_nbtor_other 0.074 r_chiral_restr 0.065 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5979 Nucleic Acid Atoms Solvent Atoms 329 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling BALBES phasing