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X-ray structure of N-methyl-L-tryptophan oxidase (MTOX)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1EL5 PDB ENTRY 1EL5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5.6 PEG4000 20%, ISOPROPANOL 20%, SODIUM CITRATE 0.1 M, PH=5.6
Crystal Properties Matthews coefficient Solvent content 2.15 42.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.188 α = 90 b = 89.809 β = 104.75 c = 91.915 γ = 90
Symmetry Space Group P 1 2 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 CCD MARMOSAIC 225 mm CCD M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 BESSY 14.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 3.2 50 92 0.1 7 2.1 21160
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 3.2 3.31 93.8 0.22 4 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 (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 1EL5 3.2 40 21754 1154 99.1 0.24 0.236 0.2323 0.313 0.2313 RANDOM 41.82
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] -1.29 2.76 -0.26 2.95
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.23 r_dihedral_angle_3_deg 20.033 r_dihedral_angle_4_deg 16.555 r_dihedral_angle_1_deg 6.703 r_angle_refined_deg 1.194 r_scangle_it 0.547 r_scbond_it 0.325 r_nbtor_refined 0.304 r_mcangle_it 0.214 r_nbd_refined 0.198
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.23 r_dihedral_angle_3_deg 20.033 r_dihedral_angle_4_deg 16.555 r_dihedral_angle_1_deg 6.703 r_angle_refined_deg 1.194 r_scangle_it 0.547 r_scbond_it 0.325 r_nbtor_refined 0.304 r_mcangle_it 0.214 r_nbd_refined 0.198 r_symmetry_vdw_refined 0.188 r_symmetry_hbond_refined 0.159 r_chiral_restr 0.158 r_xyhbond_nbd_refined 0.13 r_mcbond_it 0.111 r_bond_refined_d 0.006 r_gen_planes_refined 0.003 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_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11503 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 216
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling MOLREP phasing