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Monomeric sarcosine oxidase from Bacillus sp. (SoxB) Y254A 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 1.6 M Ammonium sulfate, 100 mM Tris-HCl buffer pH8.5
Crystal Properties Matthews coefficient Solvent content 2.12 41.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.776 α = 90 b = 69.7 β = 93.749 c = 73.665 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 1.35 42.41 93.7 0.082 0.996 8.8 4.3 150204
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 1.35 1.37 0.703 0.619 2.1
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1EL5 1.35 42.408 150178 7346 93.263 0.156 0.1554 0.1643 0.1776 0.1862 12.088
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 -0.001 -0.001 -0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.389 r_dihedral_angle_3_deg 11.943 r_dihedral_angle_1_deg 7.26 r_dihedral_angle_2_deg 6.999 r_dihedral_angle_other_2_deg 5.138 r_lrange_it 3.88 r_lrange_other 3.779 r_scangle_it 3.191 r_scangle_other 3.191 r_scbond_it 2.148
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.389 r_dihedral_angle_3_deg 11.943 r_dihedral_angle_1_deg 7.26 r_dihedral_angle_2_deg 6.999 r_dihedral_angle_other_2_deg 5.138 r_lrange_it 3.88 r_lrange_other 3.779 r_scangle_it 3.191 r_scangle_other 3.191 r_scbond_it 2.148 r_scbond_other 2.148 r_angle_refined_deg 1.998 r_mcangle_it 1.728 r_mcangle_other 1.728 r_mcbond_it 1.186 r_mcbond_other 1.185 r_angle_other_deg 0.682 r_nbd_refined 0.228 r_symmetry_nbd_other 0.198 r_nbtor_refined 0.183 r_nbd_other 0.179 r_symmetry_xyhbond_nbd_other 0.154 r_symmetry_nbd_refined 0.148 r_symmetry_xyhbond_nbd_refined 0.138 r_xyhbond_nbd_refined 0.133 r_chiral_restr 0.103 r_symmetry_nbtor_other 0.083 r_gen_planes_refined 0.013 r_bond_refined_d 0.012 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5925 Nucleic Acid Atoms Solvent Atoms 683 Heterogen Atoms 133
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing