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H55A mutant of tryptophan 2,3-dioxygenase from Xanthomonas campestris
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2NW7 PDB ENTRY 2nw7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.3 293 100mM Mes (pH 6.3), 10-12% (wt/vol) PEG 4000, 60mM MnCl2, 10mM sodium dithionite, 2mM L-Trp, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.22 44.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.222 α = 90 b = 117.606 β = 95.73 c = 139.283 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 CCD MAR CCD 165 mm 2007-01-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SRS BEAMLINE PX10.1 1.381 SRS PX10.1
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 2.15 59.66 96.9 0.1 9.5 2.4 312593 131764
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) 2.15 2.27 91.7 0.474 2.5 2.3 18137
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 2nw7 2.15 54.13 125104 6624 96.73 0.2047 0.20047 0.2005 0.28457 0.2809 RANDOM 23.189
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] 1.37 0.17 -1.05 -0.29
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.948 r_dihedral_angle_4_deg 23.088 r_dihedral_angle_3_deg 19.023 r_dihedral_angle_1_deg 7.554 r_scangle_it 5.064 r_scbond_it 3.531 r_angle_refined_deg 2.346 r_mcangle_it 1.994 r_mcbond_it 1.315 r_symmetry_hbond_refined 0.443
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.948 r_dihedral_angle_4_deg 23.088 r_dihedral_angle_3_deg 19.023 r_dihedral_angle_1_deg 7.554 r_scangle_it 5.064 r_scbond_it 3.531 r_angle_refined_deg 2.346 r_mcangle_it 1.994 r_mcbond_it 1.315 r_symmetry_hbond_refined 0.443 r_xyhbond_nbd_refined 0.371 r_nbtor_refined 0.308 r_nbd_refined 0.227 r_symmetry_vdw_refined 0.224 r_chiral_restr 0.171 r_bond_refined_d 0.028 r_gen_planes_refined 0.011
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 17638 Nucleic Acid Atoms Solvent Atoms 1016 Heterogen Atoms 419
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling AMoRE phasing