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Crystal Structure of Monomeric Sarcosine Oxidase from Bacillus sp. NS-129
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1L9F PDB ENTRY 1L9F
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 293 0.1M Tris-HCl buffer (pH 8.5), 2.0M ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.1 60
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 171.042 α = 90 b = 171.042 β = 90 c = 72.455 γ = 90
Symmetry Space Group P 41 21 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 ADSC QUANTUM 315 2004-10-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1.0000 SPring-8 BL41XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.86 50 97.8 0.095 27.8 5.6 101469 101469 1 1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.86 1.92 94.6 0.471 3.5 4.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 1L9F 1.86 8 105630 83295 4408 98.59 0.15937 0.15937 0.15769 0.1692 0.19144 0.2016 RANDOM 23.518
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] 0.02 0.02 -0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.636 r_scangle_it 3.486 r_sphericity_free 2.924 r_scbond_it 2.172 r_mcangle_it 1.554 r_sphericity_bonded 1.467 r_angle_refined_deg 1.338 r_rigid_bond_restr 1.2 r_mcbond_it 0.884 r_angle_other_deg 0.821
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.636 r_scangle_it 3.486 r_sphericity_free 2.924 r_scbond_it 2.172 r_mcangle_it 1.554 r_sphericity_bonded 1.467 r_angle_refined_deg 1.338 r_rigid_bond_restr 1.2 r_mcbond_it 0.884 r_angle_other_deg 0.821 r_nbd_other 0.25 r_symmetry_vdw_other 0.238 r_nbd_refined 0.195 r_symmetry_hbond_refined 0.193 r_xyhbond_nbd_refined 0.149 r_symmetry_vdw_refined 0.092 r_chiral_restr 0.087 r_nbtor_other 0.085 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_gen_planes_other 0.006 r_bond_other_d 0.003 r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_nbtor_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5940 Nucleic Acid Atoms Solvent Atoms 484 Heterogen Atoms 108
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling MOLREP phasing