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Heterotetrameric Sarcosine Oxidase from Corynebacterium sp. U-96 in complex with methylthio acetate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1X31 PDB ENTRY 1X31
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 293 0.1M TRIS-HCL, 1.9M AMMONIUM SULFATE, 10MM CUSO4, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.15 60.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 198.949 α = 90 b = 198.949 β = 90 c = 196.765 γ = 120
Symmetry Space Group P 65 2 2
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 RIGAKU JUPITER 210 2005-10-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL26B1 1.0000 SPring-8 BL26B1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 2.2 39.62 100 0.083 0.083 18.8 8.6 115870 30.1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.32 100 0.225 8.7 146098
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1X31 2.2 39.53 109994 5804 100 0.17155 0.16978 0.1704 0.20455 0.2059 RANDOM 27.183
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] 0.03 0.02 0.03 -0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.914 r_dihedral_angle_4_deg 16.771 r_dihedral_angle_3_deg 14.335 r_dihedral_angle_1_deg 6.645 r_scangle_it 3.914 r_scbond_it 2.631 r_angle_refined_deg 1.605 r_mcangle_it 1.502 r_mcbond_it 0.947 r_symmetry_vdw_refined 0.411
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.914 r_dihedral_angle_4_deg 16.771 r_dihedral_angle_3_deg 14.335 r_dihedral_angle_1_deg 6.645 r_scangle_it 3.914 r_scbond_it 2.631 r_angle_refined_deg 1.605 r_mcangle_it 1.502 r_mcbond_it 0.947 r_symmetry_vdw_refined 0.411 r_nbtor_refined 0.307 r_nbd_refined 0.208 r_xyhbond_nbd_refined 0.139 r_symmetry_hbond_refined 0.116 r_chiral_restr 0.113 r_bond_refined_d 0.018 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12519 Nucleic Acid Atoms Solvent Atoms 924 Heterogen Atoms 180
Software Software Software Name Purpose SPACE data collection MOLREP phasing REFMAC refinement MOSFLM data reduction SCALA data scaling