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Pyruvylated beta-D-galactosidase from Bacillus sp. HMA207, E163A mutant pyruvylated beta-D-galactose complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5YHS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.2 293 32% PEG 300, 0.1 M phosphate-citrate
Crystal Properties Matthews coefficient Solvent content 2.68 54.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 114.78 α = 90 b = 114.78 β = 90 c = 150.434 γ = 120
Symmetry Space Group P 32 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 100 CCD ADSC QUANTUM 270 2017-02-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-17A 0.9800 Photon Factory BL-17A
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 2.45 100 99.9 0.081 12.1 5.3 42682 45.897
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.45 2.49 99.9 0.855 0.621 1.6 5.1
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 (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5YHS 2.45 99.4 40594 2049 99.79 0.20925 0.20627 0.27001 0.268 RANDOM 44.497
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] 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.555 r_dihedral_angle_3_deg 19.718 r_dihedral_angle_4_deg 17.969 r_dihedral_angle_1_deg 7.387 r_long_range_B_other 6.715 r_long_range_B_refined 6.714 r_scangle_other 4.886 r_mcangle_other 4.365 r_mcangle_it 4.364 r_scbond_it 3.153
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.555 r_dihedral_angle_3_deg 19.718 r_dihedral_angle_4_deg 17.969 r_dihedral_angle_1_deg 7.387 r_long_range_B_other 6.715 r_long_range_B_refined 6.714 r_scangle_other 4.886 r_mcangle_other 4.365 r_mcangle_it 4.364 r_scbond_it 3.153 r_scbond_other 3.153 r_mcbond_it 2.856 r_mcbond_other 2.854 r_angle_refined_deg 1.737 r_angle_other_deg 1.116 r_chiral_restr 0.112 r_bond_refined_d 0.014 r_gen_planes_refined 0.007 r_bond_other_d 0.006 r_gen_planes_other 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7576 Nucleic Acid Atoms Solvent Atoms 167 Heterogen Atoms 34
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing