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Monomeric sarcosine oxidase from Bacillus sp. (SoxB) complexed with L-Thioproline
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 1.5 M Ammonium sulfate, 100 mM Tris-HCl buffer pH8.5
Crystal Properties Matthews coefficient Solvent content 2.09 41.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.876 α = 90 b = 69.401 β = 93.722 c = 73.028 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 2022-02-07 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 1.3 42.24 93.2 0.062 0.993 6.8 2.1 165675
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 1.3 1.32 0.505 0.651 1.8
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 1.3 40.505 165671 8108 92.977 0.154 0.1529 0.1629 0.1753 0.1835 14.385
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] -0.006 0.001 0.005
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.452 r_dihedral_angle_3_deg 11.511 r_dihedral_angle_1_deg 7.189 r_dihedral_angle_other_2_deg 6.912 r_dihedral_angle_2_deg 5.827 r_lrange_it 4.709 r_lrange_other 4.709 r_scangle_it 3.838 r_scangle_other 3.838 r_scbond_it 2.527
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.452 r_dihedral_angle_3_deg 11.511 r_dihedral_angle_1_deg 7.189 r_dihedral_angle_other_2_deg 6.912 r_dihedral_angle_2_deg 5.827 r_lrange_it 4.709 r_lrange_other 4.709 r_scangle_it 3.838 r_scangle_other 3.838 r_scbond_it 2.527 r_scbond_other 2.526 r_mcangle_it 1.996 r_mcangle_other 1.996 r_angle_refined_deg 1.921 r_mcbond_it 1.344 r_mcbond_other 1.344 r_angle_other_deg 0.65 r_symmetry_nbd_refined 0.297 r_nbd_other 0.257 r_nbd_refined 0.227 r_symmetry_nbd_other 0.197 r_nbtor_refined 0.182 r_xyhbond_nbd_refined 0.166 r_symmetry_xyhbond_nbd_refined 0.152 r_chiral_restr 0.097 r_symmetry_xyhbond_nbd_other 0.092 r_symmetry_nbtor_other 0.081 r_chiral_restr_other 0.064 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 5991 Nucleic Acid Atoms Solvent Atoms 622 Heterogen Atoms 169
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing