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Structure of beta-galactosidase from Desulfurococcus amyloliticus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other cryoEM structure
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 293 PEG3350, 0.1M NaCitrate
Crystal Properties Matthews coefficient Solvent content 2.62 53.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.227 α = 90 b = 140.763 β = 90 c = 207.773 γ = 90
Symmetry Space Group P 2 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 2021-12-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 0.9000 SPring-8 BL41XU
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 2.15 50 98.8 0.99 17.6 12.5 128459
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 2.15 2.19 0.75
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 2.15 15 127967 6351 98.397 0.168 0.1654 0.1749 0.2114 0.2149 42.007
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] 0.008 0.14 -0.148
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.234 r_dihedral_angle_4_deg 20.712 r_dihedral_angle_3_deg 16.422 r_lrange_other 8.356 r_lrange_it 8.352 r_dihedral_angle_1_deg 8.196 r_scangle_it 6.618 r_scangle_other 6.618 r_mcangle_it 4.864 r_mcangle_other 4.864
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.234 r_dihedral_angle_4_deg 20.712 r_dihedral_angle_3_deg 16.422 r_lrange_other 8.356 r_lrange_it 8.352 r_dihedral_angle_1_deg 8.196 r_scangle_it 6.618 r_scangle_other 6.618 r_mcangle_it 4.864 r_mcangle_other 4.864 r_scbond_it 4.436 r_scbond_other 4.436 r_mcbond_it 3.507 r_mcbond_other 3.506 r_angle_refined_deg 1.643 r_angle_other_deg 1.255 r_symmetry_xyhbond_nbd_refined 0.223 r_nbd_refined 0.197 r_symmetry_nbd_other 0.186 r_nbd_other 0.179 r_symmetry_nbd_refined 0.17 r_nbtor_refined 0.166 r_xyhbond_nbd_refined 0.156 r_symmetry_nbtor_other 0.077 r_chiral_restr 0.071 r_symmetry_xyhbond_nbd_other 0.053 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 15709 Nucleic Acid Atoms Solvent Atoms 451 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing