☰ Navigation Tabs
Monomeric sarcosine oxidase from Bacillus sp. (SoxB) complexed with D-Proline
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 2.06 40.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.367 α = 90 b = 69.687 β = 92.096 c = 73.095 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 1.35 41.67 97.1 0.035 0.997 9 1.9 151911
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 0.502 0.614 1.4
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 41.67 151888 8068 96.833 0.159 0.1579 0.1578 0.1828 0.1828 18.318
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] 0.001 0.001 -0.002 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_other_2_deg 27.856 r_dihedral_angle_6_deg 14.946 r_dihedral_angle_2_deg 12.167 r_dihedral_angle_3_deg 12.113 r_dihedral_angle_1_deg 7.162 r_lrange_it 5.837 r_lrange_other 5.837 r_scangle_it 4.562 r_scangle_other 4.497 r_scbond_it 3.017
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_other_2_deg 27.856 r_dihedral_angle_6_deg 14.946 r_dihedral_angle_2_deg 12.167 r_dihedral_angle_3_deg 12.113 r_dihedral_angle_1_deg 7.162 r_lrange_it 5.837 r_lrange_other 5.837 r_scangle_it 4.562 r_scangle_other 4.497 r_scbond_it 3.017 r_scbond_other 2.978 r_mcangle_other 2.222 r_mcangle_it 2.221 r_angle_refined_deg 1.952 r_mcbond_it 1.63 r_mcbond_other 1.618 r_angle_other_deg 0.658 r_nbd_refined 0.23 r_symmetry_nbd_other 0.201 r_symmetry_nbd_refined 0.197 r_nbtor_refined 0.184 r_nbd_other 0.184 r_xyhbond_nbd_refined 0.164 r_symmetry_xyhbond_nbd_refined 0.143 r_chiral_restr 0.098 r_symmetry_nbtor_other 0.082 r_chiral_restr_other 0.026 r_gen_planes_refined 0.013 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 5940 Nucleic Acid Atoms Solvent Atoms 458 Heterogen Atoms 168
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing