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Structural insight into bioremediation of triphenylmethane dyes by Citrobacter sp. triphenylmethane reductase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2VRB PDB ENTRY 2VRB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8 0.05 M KH2PO4, 18% PEG8000, 10 MM NADP
Crystal Properties Matthews coefficient Solvent content 2.64 53.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.262 α = 90 b = 140.384 β = 90 c = 76.096 γ = 90
Symmetry Space Group C 2 2 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 CCD 2008-07-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 6C1 PAL/PLS 6C1
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 1.96 50 95.9 0.08 28.85 11.7 22401 -0.5
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 1.96 2.02 83.3 0.4 2.81 7.8
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 2VRB 1.96 30 21246 1142 95.9 0.182 0.179 0.1798 0.232 0.2333 RANDOM 28.72
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] 1.86 -1.33 -0.54
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.019 r_dihedral_angle_3_deg 14.352 r_dihedral_angle_4_deg 9.537 r_dihedral_angle_1_deg 5.829 r_scangle_it 3.432 r_scbond_it 2.211 r_angle_refined_deg 1.379 r_mcangle_it 1.304 r_mcbond_it 0.883 r_nbtor_refined 0.301
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.019 r_dihedral_angle_3_deg 14.352 r_dihedral_angle_4_deg 9.537 r_dihedral_angle_1_deg 5.829 r_scangle_it 3.432 r_scbond_it 2.211 r_angle_refined_deg 1.379 r_mcangle_it 1.304 r_mcbond_it 0.883 r_nbtor_refined 0.301 r_symmetry_hbond_refined 0.252 r_nbd_refined 0.211 r_symmetry_vdw_refined 0.2 r_xyhbond_nbd_refined 0.154 r_chiral_restr 0.09 r_bond_refined_d 0.013 r_gen_planes_refined 0.005 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 2189 Nucleic Acid Atoms Solvent Atoms 167 Heterogen Atoms 78
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing