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Ferredoxin component of 3-nitrotoluene dioxygenase from Diaphorobacter sp. strain DS2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2QPZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 277 200mM calcium chloride, 100mM HEPES pH 7.5, 25-28% PEG 400
Crystal Properties Matthews coefficient Solvent content 3.75 67.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.53 α = 90 b = 79.53 β = 90 c = 108.97 γ = 90
Symmetry Space Group I 4 2 2
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 2014-06-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.873 ESRF ID23-1
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 2.1 56.27 99.9 0.063 0.022 17.28 8.6 10628 48.39
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.21 99.3 8.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 2QPZ 2.4 13.74 1.46 7088 336 99.12 0.2328 0.2312 0.2341 0.2619 0.2611 Random
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 15.896 f_angle_d 1.344 f_chiral_restr 0.052 f_bond_d 0.011 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 785 Nucleic Acid Atoms Solvent Atoms 15 Heterogen Atoms 5
Software Software Software Name Purpose PHENIX refinement MOSFLM data reduction SCALA data scaling d*TREK phasing