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Monomeric sarcosine oxidase from Bacillus sp. (SoxB) Y254G mutant
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1EL5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 1.8 M Ammonium sulfate, 100 mM Tris-HCl buffer pH8.5
Crystal Properties Matthews coefficient Solvent content 2.11 41.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.58 α = 90 b = 69.673 β = 93.735 c = 73.676 γ = 90
Symmetry Space Group P 1 21 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 PIXEL DECTRIS EIGER X 16M 2022-06-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.9 SPring-8 BL44XU
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 1.45 42.364 99 0.078 0.998 11.4 5.4 128302
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 1.45 1.47 0.777 0.765 2.6
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-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1EL5 1.45 42.364 128280 6788 98.929 0.161 0.1595 0.1688 0.1857 0.1921 13.636
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] -0.003 0.003 0.003 -0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.943 r_dihedral_angle_3_deg 11.862 r_dihedral_angle_2_deg 7.436 r_dihedral_angle_1_deg 7.178 r_dihedral_angle_other_2_deg 4.585 r_lrange_it 4.241 r_lrange_other 4.144 r_scangle_it 3.48 r_scangle_other 3.48 r_scbond_other 2.327
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.943 r_dihedral_angle_3_deg 11.862 r_dihedral_angle_2_deg 7.436 r_dihedral_angle_1_deg 7.178 r_dihedral_angle_other_2_deg 4.585 r_lrange_it 4.241 r_lrange_other 4.144 r_scangle_it 3.48 r_scangle_other 3.48 r_scbond_other 2.327 r_scbond_it 2.326 r_mcangle_other 1.943 r_mcangle_it 1.939 r_angle_refined_deg 1.872 r_mcbond_it 1.32 r_mcbond_other 1.319 r_angle_other_deg 0.654 r_nbd_refined 0.208 r_symmetry_nbd_other 0.192 r_nbtor_refined 0.184 r_nbd_other 0.16 r_symmetry_xyhbond_nbd_refined 0.139 r_xyhbond_nbd_refined 0.137 r_symmetry_nbd_refined 0.124 r_chiral_restr 0.097 r_symmetry_nbtor_other 0.082 r_symmetry_xyhbond_nbd_other 0.076 r_gen_planes_refined 0.012 r_bond_refined_d 0.011 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5906 Nucleic Acid Atoms Solvent Atoms 645 Heterogen Atoms 126
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing