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Naphthalene 1,2-dioxygenase Rieske ferredoxin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1FQT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 282 36-38% PEG8000, 100 mM MES, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 282K
Crystal Properties Matthews coefficient Solvent content 2.68 54.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.23 α = 90 b = 65.23 β = 90 c = 49.44 γ = 120
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 210 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 0.934000 ESRF ID14-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.85 58.5 99.6 0.063 0.063 8 14.2 10291
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.85 1.95 97.5 0.249 0.249 2.9 7.7 1446
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 1FQT 1.85 28.25 10268 493 99.48 0.157 0.154 0.1557 0.197 0.2071 RANDOM 24.734
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 0.65 1.29 -1.94
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.779 r_dihedral_angle_4_deg 19.843 r_dihedral_angle_3_deg 17.528 r_sphericity_free 10.523 r_sphericity_bonded 7.483 r_scangle_it 6.619 r_dihedral_angle_1_deg 6.552 r_scbond_it 4.986 r_mcangle_it 3.764 r_rigid_bond_restr 3.342
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.779 r_dihedral_angle_4_deg 19.843 r_dihedral_angle_3_deg 17.528 r_sphericity_free 10.523 r_sphericity_bonded 7.483 r_scangle_it 6.619 r_dihedral_angle_1_deg 6.552 r_scbond_it 4.986 r_mcangle_it 3.764 r_rigid_bond_restr 3.342 r_mcbond_it 3.132 r_angle_refined_deg 2.372 r_mcbond_other 1.453 r_angle_other_deg 1.309 r_xyhbond_nbd_refined 0.338 r_nbd_other 0.265 r_symmetry_hbond_refined 0.265 r_nbd_refined 0.249 r_symmetry_vdw_other 0.204 r_nbtor_refined 0.182 r_chiral_restr 0.15 r_symmetry_vdw_refined 0.099 r_nbtor_other 0.094 r_bond_refined_d 0.025 r_bond_other_d 0.011 r_gen_planes_refined 0.01 r_gen_planes_other 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 818 Nucleic Acid Atoms Solvent Atoms 98 Heterogen Atoms 4
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling AMoRE phasing REFMAC refinement PDB_EXTRACT data extraction