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Rat cysteine dioxygenase with cysteine persulfide bound to active site iron
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3ELN PDB entry 3eln
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 297 Hanging drops of 1.5 microL of approximately 8 mg/mL CDO and 1.5 microL reservoir buffer were allowed to equilibrate above the reservoir buffer (24-34% (w/v) polyethylene glycol 4000, 100-250 mM ammonium acetate, 100 mM sodium citrate, 0-4 mM dithionite, 40 mM L-cysteine). Crystals grew as needles or starbursts of approximately 0.1 mm in length in one week, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 297K
Crystal Properties Matthews coefficient Solvent content 2.22 44.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.75 α = 90 b = 57.75 β = 90 c = 122.67 γ = 90
Symmetry Space Group P 43 21 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 210r Double Si with sagittaly bent second crystal 2012-03-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX1 0.95370 Australian Synchrotron MX1
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 1.95 52.25 99.9 0.042 67.5 16.1 15914 15914 1.75 19.2
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 1.95 2.05 99.8 0.213 17.5 16.9 2257
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 3eln 1.95 33.99 15876 15053 807 99.77 0.19288 0.19137 0.1914 0.22194 0.2225 The same R-free flags as PDB 3eln 21.459
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] -0.19 -0.19 0.38
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.74 r_dihedral_angle_3_deg 13.967 r_dihedral_angle_4_deg 12.413 r_dihedral_angle_1_deg 5.835 r_angle_refined_deg 1.377 r_chiral_restr 0.103 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.74 r_dihedral_angle_3_deg 13.967 r_dihedral_angle_4_deg 12.413 r_dihedral_angle_1_deg 5.835 r_angle_refined_deg 1.377 r_chiral_restr 0.103 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_it r_mcbond_other r_mcangle_it r_scbond_it 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 1519 Nucleic Acid Atoms Solvent Atoms 177 Heterogen Atoms 9
Software Software Software Name Purpose Blu-Ice data collection PHASER phasing REFMAC refinement MOSFLM data reduction SCALA data scaling