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Crystal structure of tryptophan oxidase (C395A mutant) from Chromobacterium violaceum
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 293 0.1M MES, 40% Polyethylene glycol 400, pH6.8
Crystal Properties Matthews coefficient Solvent content 2.36 47.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.86 α = 90 b = 89.27 β = 90 c = 112.7 γ = 90
Symmetry Space Group P 21 21 21
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 270 2014-06-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1 Photon Factory AR-NW12A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 1.8 69.98 100 0.095 0.103 14.45 7.325 82681 26.033
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.9 100 0.274 0.295 6.82 7.341
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.8 69.98 78540 4141 99.97 0.15981 0.15755 0.1699 0.20225 0.2106 RANDOM 22.401
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] 0.37 0.16 -0.53
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.223 r_dihedral_angle_4_deg 17.923 r_dihedral_angle_3_deg 13.609 r_long_range_B_refined 6.604 r_long_range_B_other 6.429 r_dihedral_angle_1_deg 6.109 r_scangle_other 4.741 r_scbond_it 3.079 r_scbond_other 3.078 r_mcangle_it 2.889
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.223 r_dihedral_angle_4_deg 17.923 r_dihedral_angle_3_deg 13.609 r_long_range_B_refined 6.604 r_long_range_B_other 6.429 r_dihedral_angle_1_deg 6.109 r_scangle_other 4.741 r_scbond_it 3.079 r_scbond_other 3.078 r_mcangle_it 2.889 r_mcangle_other 2.889 r_mcbond_it 2.024 r_mcbond_other 2.023 r_angle_refined_deg 1.832 r_angle_other_deg 0.9 r_chiral_restr 0.12 r_bond_refined_d 0.018 r_gen_planes_refined 0.014 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6452 Nucleic Acid Atoms Solvent Atoms 760 Heterogen Atoms 136
Software Software Software Name Purpose REFMAC refinement XSCALE data scaling MOLREP phasing PDB_EXTRACT data extraction XDS data reduction